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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Étienne Mollier pushed to branch upstream at <a href="https://salsa.debian.org/med-team/python-bcbio-gff">Debian Med / python-bcbio-gff</a>
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Commits:
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410">112984ef</a></strong>
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<span> by Étienne Mollier </span> <i> at 2023-07-12T21:56:46+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 0.7.0</pre>
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30 changed files:
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BCBio/GFF/__init__.py
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<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
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<li id="ba3404825a4d349f45211497986428bd4b75a757">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#ba3404825a4d349f45211497986428bd4b75a757"><strong style="font-weight: bold;">BCBio/GFF/GFFParser.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -31,7 +31,15 @@ except AttributeError:</td>
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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC31" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_utils</span></span>
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<td class="old_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">collections</span><span class="p">.</span><span class="n" style="color: #333;">defaultdict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_utils</span><span class="p">.</span><span class="n" style="color: #333;">defaultdict</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC33" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC34" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">UnknownSeq</span></span>
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<td class="old_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="python"><span class="n" style="color: #333;">unknown_seq_avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="old_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">UnknownSeq</span></span>
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<td class="old_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">unknown_seq_avail</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="old_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Starting with biopython 1.81, has been removed</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_UndefinedSequenceData</span></span>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="python"></span>
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35
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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
43
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC43" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>
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36
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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
44
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC44" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqFeature</span></span>
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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
37
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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
45
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC45" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -69,7 +77,7 @@ def _gff_line_map(line, params):</td>
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<td class="old_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
69
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<td class="new_line diff-line-num" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
77
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC77" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
70
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<td class="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
78
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> GFF3 has key value pairs like:</span></span>
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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
71
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<td class="new_line diff-line-num" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
79
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;"> count=9;gene=amx-2;sequence=SAGE:aacggagccg</span></span>
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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
72
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<td class="new_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> GFF2 and GTF have:<span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
80
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> GFF2 and GTF have:</span></span>
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<td class="old_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
73
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<td class="new_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
81
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> Sequence "Y74C9A" ; Note "Clone Y74C9A; Genbank AC024206"</span></span>
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<td class="old_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
74
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<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
82
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;"> name "fgenesh1_pg.C_chr_1000003"; transcriptId 869</span></span>
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<td class="old_line diff-line-num" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
75
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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
83
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -170,7 +178,7 @@ def _gff_line_map(line, params):</td>
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170
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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
178
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">should_do</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
171
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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
179
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">limit_info</span><span class="p">:</span></span>
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172
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180
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">limit_name</span><span class="p">,</span> <span class="n" style="color: #333;">limit_values</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">limit_info</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">items</span><span class="p">():</span></span>
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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
173
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<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">cur_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">tuple</span><span class="p">([</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
181
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">cur_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">tuple</span><span class="p">([</span><span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<td class="old_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
174
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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
182
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">filter_info</span><span class="p">[</span><span class="n" style="color: #333;">limit_name</span><span class="p">]])</span></span>
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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
175
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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
183
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cur_id</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">limit_values</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
176
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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
184
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">should_do</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -286,7 +294,7 @@ class _AbstractMapReduceGFF:</td>
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<td class="old_line diff-line-num" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
286
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<td class="new_line diff-line-num" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
294
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;"> information.</span></span>
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<td class="old_line diff-line-num" data-linenumber="287" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
287
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<td class="new_line diff-line-num" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
295
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC295" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
288
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<td class="new_line diff-line-num" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
296
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">create_missing</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
289
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<td class="new_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC289" class="line" lang="python"> <span class="s" style="color: #d14;">"""Initialize GFF parser<span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC297" class="line" lang="python"> <span class="s" style="color: #d14;">"""Initialize GFF parser</span></span>
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<td class="old_line diff-line-num" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
290
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<td class="new_line diff-line-num" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
298
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC298" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
291
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<td class="new_line diff-line-num" data-linenumber="299" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
299
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC299" class="line" lang="python"><span class="s" style="color: #d14;"> create_missing - If True, create blank records for GFF ids not in</span></span>
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<td class="old_line diff-line-num" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
292
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<td class="new_line diff-line-num" data-linenumber="300" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
300
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC300" class="line" lang="python"><span class="s" style="color: #d14;"> the base_dict. If False, an error will be raised.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -305,7 +313,7 @@ class _AbstractMapReduceGFF:</td>
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<td class="old_line diff-line-num" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
305
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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
313
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;"> limit_info - A dictionary specifying the regions of the GFF file</span></span>
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<td class="old_line diff-line-num" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
306
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<td class="new_line diff-line-num" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
314
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;"> which should be extracted. This allows only relevant portions of a file</span></span>
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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
307
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<td class="new_line diff-line-num" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
315
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;"> to be parsed.</span></span>
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308
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC308" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
316
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC316" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
309
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<td class="new_line diff-line-num" data-linenumber="317" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
317
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;"> base_dict - A base dictionary of SeqRecord objects which may be</span></span>
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<td class="old_line diff-line-num" data-linenumber="310" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
310
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<td class="new_line diff-line-num" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
318
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;"> pre-populated with sequences and other features. The new features from</span></span>
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311
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<td class="new_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
319
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;"> the GFF file will be added to this dictionary.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="536" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -536,11 +544,16 @@ class _AbstractMapReduceGFF:</td>
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<td class="old_line diff-line-num" data-linenumber="536" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
536
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<td class="new_line diff-line-num" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
544
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC544" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match_id</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="537" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
537
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<td class="new_line diff-line-num" data-linenumber="545" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
545
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC545" class="line" lang="python"> <span class="n" style="color: #333;">cur_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">match_id</span><span class="p">]</span></span>
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538
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<td class="new_line diff-line-num" data-linenumber="546" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
546
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC546" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># update generated unknown sequences with the expected maximum length</span></span>
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<td class="old_line diff-line-num old" data-linenumber="539" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
539
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<td class="new_line diff-line-num old" data-linenumber="547" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC539" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">UnknownSeq</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="547" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
547
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC547" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left addition" style="background-color: #c7f0d2;">unknown_seq_avail</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="ow" style="font-weight: 600;"><span class="idiff addition" style="background-color: #c7f0d2;">and</span></span><span class="idiff right addition" style="background-color: #c7f0d2;"> </span><span class="nf" style="color: #900; font-weight: 600;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">UnknownSeq</span><span class="p">):</span></span>
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540
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<td class="new_line diff-line-num" data-linenumber="548" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
548
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">([</span><span class="n" style="color: #333;">max_loc</span><span class="p">,</span> <span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">_length</span><span class="p">])</span></span>
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<td class="old_line diff-line-num new" data-linenumber="541" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
549
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">unknown_seq_avail</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nf" style="color: #900; font-weight: 600;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">_data</span><span class="p">,</span> <span class="n" style="color: #333;">_UndefinedSequenceData</span><span class="p">):</span></span>
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<td class="old_line diff-line-num new" data-linenumber="541" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
550
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">_data</span><span class="p">.</span><span class="n" style="color: #333;">_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">([</span><span class="n" style="color: #333;">max_loc</span><span class="p">,</span> <span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">_data</span><span class="p">.</span><span class="n" style="color: #333;">_length</span><span class="p">])</span></span>
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541
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<td class="new_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
551
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_rec</span><span class="p">,</span> <span class="n" style="color: #333;">base</span></span>
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542
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<td class="new_line diff-line-num" data-linenumber="552" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
552
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_create_missing</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="543" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
543
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<td class="new_line diff-line-num old" data-linenumber="553" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;">new_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SeqRecord</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">UnknownSeq</span><span class="p">(</span><span class="n" style="color: #333;">max_loc</span><span class="p">),</span> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">])</span></span>
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<td class="new_line diff-line-num new" data-linenumber="553" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
553
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">unknown_seq_avail</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="554" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
554
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">new_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SeqRecord</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">UnknownSeq</span><span class="p">(</span><span class="n" style="color: #333;">max_loc</span><span class="p">),</span> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">])</span></span>
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<td class="old_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="555" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
555
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="556" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
556
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">new_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SeqRecord</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">Seq</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_loc</span><span class="p">),</span> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">])</span></span>
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<td class="old_line diff-line-num" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
544
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<td class="new_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
557
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_rec</span></span>
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<td class="old_line diff-line-num" data-linenumber="545" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
545
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<td class="new_line diff-line-num" data-linenumber="558" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
558
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC558" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_rec</span><span class="p">,</span> <span class="n" style="color: #333;">base</span></span>
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546
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<td class="new_line diff-line-num" data-linenumber="559" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
559
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="654" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="667" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -654,7 +667,7 @@ class GFFParser(_AbstractMapReduceGFF):</td>
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<td class="old_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
654
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<td class="new_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
667
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC667" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">line_adjust_fn</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">create_missing</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
655
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<td class="new_line diff-line-num" data-linenumber="668" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
668
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC668" class="line" lang="python"> <span class="n" style="color: #333;">_AbstractMapReduceGFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">create_missing</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">create_missing</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
656
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<td class="new_line diff-line-num" data-linenumber="669" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
669
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC669" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_line_adjust_fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_adjust_fn</span></span>
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<td class="old_line diff-line-num old" data-linenumber="657" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
657
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<td class="new_line diff-line-num old" data-linenumber="670" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC657" class="line" lang="python"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="658" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
670
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC670" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
658
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<td class="new_line diff-line-num" data-linenumber="671" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
671
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC671" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_gff_process</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">gff_files</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="p">,</span> <span class="n" style="color: #333;">target_lines</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="659" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
659
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<td class="new_line diff-line-num" data-linenumber="672" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
672
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC672" class="line" lang="python"> <span class="s" style="color: #d14;">"""Process GFF addition without any parallelization.</span></span>
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<td class="old_line diff-line-num" data-linenumber="660" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
660
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<td class="new_line diff-line-num" data-linenumber="673" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
673
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC673" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="717" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -704,7 +717,7 @@ class GFFParser(_AbstractMapReduceGFF):</td>
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<td class="old_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
704
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<td class="new_line diff-line-num" data-linenumber="717" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
717
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC717" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">out_info</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_results</span><span class="p">()</span></span>
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705
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<td class="new_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
718
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">out_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">_GFFParserLocalOut</span><span class="p">((</span><span class="n" style="color: #333;">target_lines</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span></span>
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706
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<td class="new_line diff-line-num" data-linenumber="719" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
719
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC719" class="line" lang="python"> <span class="n" style="color: #333;">target_lines</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="707" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
707
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<td class="new_line diff-line-num old" data-linenumber="720" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC707" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333;">results</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'directive'</span> <span class="ow" style="font-weight: 600;">and</span><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
720
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC720" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">if </span><span class="p">(</span><span class="n" style="color: #333;">results</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'directive'</span> <span class="ow" style="font-weight: 600;">and</span></span>
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708
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<td class="new_line diff-line-num" data-linenumber="721" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
721
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC721" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'FASTA'</span><span class="p">):</span></span>
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709
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<td class="new_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
722
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC722" class="line" lang="python"> <span class="n" style="color: #333;">found_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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710
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723
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC723" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -741,7 +754,7 @@ class DiscoGFFParser(_AbstractMapReduceGFF):</td>
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<td class="new_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC754" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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742
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<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
755
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC755" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">disco_host</span><span class="p">,</span> <span class="n" style="color: #333;">create_missing</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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743
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<td class="new_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
756
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC756" class="line" lang="python"> <span class="s" style="color: #d14;">"""Initialize parser.</span></span>
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<td class="new_line diff-line-num old" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC744" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC757" class="line" lang="python"></span>
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<td class="new_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
758
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC758" class="line" lang="python"><span class="s" style="color: #d14;"> disco_host - Web reference to a Disco host which will be used for</span></span>
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<td class="new_line diff-line-num" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
759
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC759" class="line" lang="python"><span class="s" style="color: #d14;"> parallelizing the GFF reading job.</span></span>
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760
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC760" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="768" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -755,7 +768,7 @@ class DiscoGFFParser(_AbstractMapReduceGFF):</td>
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755
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768
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC768" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># make these imports local; only need them when using disco</span></span>
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769
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC769" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">simplejson</span></span>
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<td class="old_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
757
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<td class="new_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
770
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC770" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">disco</span></span>
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<td class="old_line diff-line-num old" data-linenumber="758" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
758
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<td class="new_line diff-line-num old" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC758" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># absolute path names unless they are special disco files<span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
771
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC771" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># absolute path names unless they are special disco files</span></span>
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<td class="old_line diff-line-num" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
759
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<td class="new_line diff-line-num" data-linenumber="772" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
772
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC772" class="line" lang="python"> <span class="n" style="color: #333;">full_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num" data-linenumber="760" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
760
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<td class="new_line diff-line-num" data-linenumber="773" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
773
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gff_files</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
761
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<td class="new_line diff-line-num" data-linenumber="774" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
774
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC774" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"disco"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="829" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="842" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -829,7 +842,7 @@ class GFFExaminer:</td>
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<td class="old_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
829
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<td class="new_line diff-line-num" data-linenumber="842" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
842
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC842" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="830" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
830
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<td class="new_line diff-line-num" data-linenumber="843" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
843
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC843" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_filter_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span><span class="n" style="color: #333;">gff_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">gff_source_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">],</span></span>
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<td class="old_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
831
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<td class="new_line diff-line-num" data-linenumber="844" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
844
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC844" class="line" lang="python"> <span class="n" style="color: #333;">gff_source</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">gff_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<td class="old_line diff-line-num old" data-linenumber="832" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
832
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<td class="new_line diff-line-num old" data-linenumber="845" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC832" class="line" lang="python"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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<td class="old_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="845" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
845
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC845" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="833" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
833
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<td class="new_line diff-line-num" data-linenumber="846" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
846
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC846" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_local_params</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="834" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
834
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<td class="new_line diff-line-num" data-linenumber="847" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
847
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC847" class="line" lang="python"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_LocalParams</span><span class="p">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
835
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<td class="new_line diff-line-num" data-linenumber="848" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
848
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC848" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="838" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="851" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -838,13 +851,13 @@ class GFFExaminer:</td>
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<td class="old_line diff-line-num" data-linenumber="838" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
838
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<td class="new_line diff-line-num" data-linenumber="851" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
851
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC851" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">limit_info</span></span>
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<td class="old_line diff-line-num" data-linenumber="839" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
839
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<td class="new_line diff-line-num" data-linenumber="852" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
852
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC852" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">filter_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_filter_info</span></span>
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840
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853
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC853" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">params</span></span>
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841
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC841" class="line" lang="python"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span>
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854
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC854" class="line" lang="python"></span>
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842
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<td class="new_line diff-line-num" data-linenumber="855" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
855
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC855" class="line" lang="python"> <span class="nd">@_file_or_handle</span></span>
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<td class="old_line diff-line-num" data-linenumber="843" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
843
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<td class="new_line diff-line-num" data-linenumber="856" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
856
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC856" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">available_limits</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">gff_handle</span><span class="p">):</span></span>
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<td class="old_line diff-line-num" data-linenumber="844" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
844
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<td class="new_line diff-line-num" data-linenumber="857" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
857
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC857" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return dictionary information on possible limits for this file.</span></span>
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845
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858
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC858" class="line" lang="python"></span>
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846
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<td class="new_line diff-line-num" data-linenumber="859" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
859
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC859" class="line" lang="python"><span class="s" style="color: #d14;"> This returns a nested dictionary with the following structure:</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC847" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
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860
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC860" class="line" lang="python"></span>
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848
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<td class="new_line diff-line-num" data-linenumber="861" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
861
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC861" class="line" lang="python"><span class="s" style="color: #d14;"> keys -- names of items to filter by</span></span>
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862
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC862" class="line" lang="python"><span class="s" style="color: #d14;"> values -- dictionary with:</span></span>
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863
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC863" class="line" lang="python"><span class="s" style="color: #d14;"> keys -- filter choice</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="884" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="897" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -884,7 +897,7 @@ class GFFExaminer:</td>
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884
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897
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC897" class="line" lang="python"></span>
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<td class="old_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
885
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<td class="new_line diff-line-num" data-linenumber="898" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
898
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC898" class="line" lang="python"><span class="s" style="color: #d14;"> keys -- tuple of (source, type) for each parent</span></span>
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<td class="old_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
886
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<td class="new_line diff-line-num" data-linenumber="899" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
899
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC899" class="line" lang="python"><span class="s" style="color: #d14;"> values -- tuple of (source, type) as children of that parent</span></span>
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887
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC887" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right deletion" style="background-color: #fac5cd;"> </span></span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC900" class="line" lang="python"></span>
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901
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC901" class="line" lang="python"><span class="s" style="color: #d14;"> Not a parallelized map-reduce implementation.</span></span>
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889
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<td class="new_line diff-line-num" data-linenumber="902" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
902
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC902" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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890
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<td class="new_line diff-line-num" data-linenumber="903" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
903
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC903" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># collect all of the parent and child types mapped to IDs</span></span>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#377317303b32a87f51356a964b30d05b7cf78ba3"><strong style="font-weight: bold;">BCBio/GFF/__init__.py</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -3,4 +3,4 @@</td>
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3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio.GFF.GFFParser</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFFParser</span><span class="p">,</span> <span class="n" style="color: #333;">DiscoGFFParser</span><span class="p">,</span> <span class="n" style="color: #333;">GFFExaminer</span><span class="p">,</span> <span class="n" style="color: #333;">parse</span><span class="p">,</span> <span class="n" style="color: #333;">parse_simple</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio.GFF.GFFOutput</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF3Writer</span><span class="p">,</span> <span class="n" style="color: #333;">write</span></span>
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5
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5
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="python"></span>
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6
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.<span class="idiff left right deletion" style="background-color: #fac5cd;">6.9</span>"</span></span></pre></td>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.<span class="idiff left right addition" style="background-color: #c7f0d2;">7.0</span>"</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong style="font-weight: bold;">PKG-INFO</strong></a>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">Metadata-Version: <span class="idiff left right deletion" style="background-color: #fac5cd;">1.0</span></span>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">Metadata-Version: <span class="idiff left right addition" style="background-color: #c7f0d2;">2.1</span></span>
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2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext">Name: bcbio-gff</span>
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right deletion" style="background-color: #fac5cd;">6.9</span></span>
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3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right addition" style="background-color: #c7f0d2;">7.0</span></span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="plaintext">Summary: Read and write Generic Feature Format (GFF) with Biopython integration.</span>
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/chapmanb/bcbb/tree/master/gff</span>
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="plaintext">Author: Brad Chapman</span>
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="plaintext">Author-email: chapmanb@50mail.com</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="plaintext">License: Biopython License</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">Description: UNKNOWN</span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">Platform: UNKNOWN</span></pre></td>
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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext">License-File: LICENSE</span></pre></td>
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<li id="05ff4d05b4718a5c1e7de6afef599c230c721357">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#05ff4d05b4718a5c1e7de6afef599c230c721357"><strong style="font-weight: bold;">Scripts/gff/access_gff_index.py</strong>
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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""Access an GFF file using bx-python's interval indexing.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">Requires:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;"> bx-python: http://bitbucket.org/james_taylor/bx-python/wiki/Home</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> gff library: http://github.com/chapmanb/bcbb/tree/master/gff</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">Index time:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;"> 44 Mb file</span></span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;"> 11 seconds</span></span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;"> Index is 7.5Mb</span></span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">with_statement</span></span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="python"></span>
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16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">bx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">interval_index_file</span></span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">gff_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff_file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".index"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exists</span><span class="p">(</span><span class="n" style="color: #333;">gff_index</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Indexing GFF file"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">index</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFIndexedAccess</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">keep_open</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">seqids</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">feature</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_features_in_region</span><span class="p">(</span><span class="s" style="color: #d14;">"Chr2"</span><span class="p">,</span> <span class="mi" style="color: #099;">17500</span><span class="p">,</span> <span class="mi" style="color: #099;">20000</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">feature</span></span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">feature</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_features_in_region</span><span class="p">(</span><span class="s" style="color: #d14;">"Chr5"</span><span class="p">,</span> <span class="mi" style="color: #099;">500000</span><span class="p">,</span> <span class="mi" style="color: #099;">502500</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">feature</span></span>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
33
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">exam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">GFFExaminer</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
34
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print exam.available_limits(gff_file)</span></span>
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35
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print exam.parent_child_map(gff_file)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
36
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
37
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
38
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
39
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">gff_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"protein"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gene"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mRNA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">,</span> <span class="s" style="color: #d14;">"five_prime_UTR"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
40
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"three_prime_UTR"</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
41
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="python"> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
42
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">feature</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_features_in_region</span><span class="p">(</span><span class="s" style="color: #d14;">"Chr1"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">50000</span><span class="p">,</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
43
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">limit_info</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
44
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
45
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">found</span></span>
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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
46
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
47
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GFFIndexedAccess</span><span class="p">(</span><span class="n" style="color: #333;">interval_index_file</span><span class="p">.</span><span class="n" style="color: #333;">AbstractIndexedAccess</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
48
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"""Provide indexed access to a GFF file.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
49
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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50
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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51
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">interval_index_file</span><span class="p">.</span><span class="n" style="color: #333;">AbstractIndexedAccess</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span></span>
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52
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
53
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
54
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
55
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="python"> <span class="nd">@property</span></span>
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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
56
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">seqids</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
57
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">indexes</span><span class="p">.</span><span class="n" style="color: #333;">indexes</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
58
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
59
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_features_in_region</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
60
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">"""Retrieve features located on a given region in start/end coordinates.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
61
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
62
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_normalize_limit_info</span><span class="p">(</span><span class="n" style="color: #333;">limit_info</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
63
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">line_gen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get_as_iterator</span><span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
64
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
65
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">results</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_lines_to_out_info</span><span class="p">(</span><span class="n" style="color: #333;">line_gen</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
66
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">recs</span><span class="p">,</span> <span class="s" style="color: #d14;">"Unexpected multiple results"</span></span>
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67
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_results_to_features</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(),</span> <span class="n" style="color: #333;">results</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
68
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">recs</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
69
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
70
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
71
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
72
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="n" style="color: #333;">seqid</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span></span>
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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
74
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
75
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_at_current_offset</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">,</span> <span class="n" style="color: #333;">handle</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
76
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">readline</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
77
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">line</span></span>
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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
78
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC78" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
79
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">index</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">index_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
80
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interval_index_file</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">Indexes</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
81
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">in_handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
82
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
83
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">tell</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
84
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">readline</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
85
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
86
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
87
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
88
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
89
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC89" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="n" style="color: #333;">gtype</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parts</span><span class="p">[:</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
90
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">),</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
91
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
92
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff_file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".index"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
93
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">index_handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
94
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">index_handle</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
95
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">index_file</span></span>
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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
96
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC96" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
97
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC97" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
98
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC98" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span></pre></td>
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<li id="41731cf6f4dd9bb65e654cdbac1505e47ccb8f13">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#41731cf6f4dd9bb65e654cdbac1505e47ccb8f13"><strong style="font-weight: bold;">Scripts/gff/genbank_to_gff.py</strong>
deleted</a>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Convert a GenBank file into GFF format.</span></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="python"></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> genbank_to_gff.py <genbank_file></span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">gb_file</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%s.gff"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">gb_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out_handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">gb_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"genbank"</span><span class="p">),</span> <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>
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19
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="python"></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#2886ed2cda7201b9be162bae766fb9ce71abbc0d"><strong style="font-weight: bold;">Scripts/gff/gff2_to_gff3.py</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Convert a GFF2 file to an updated GFF3 format file.</span></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="python"></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> gff2_to_gff3.py <in_gff2_file></span></span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">The output file has the same name with the extension gff3.</span></span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio.GFF</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFFParser</span><span class="p">,</span> <span class="n" style="color: #333;">GFF3Writer</span></span>
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13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%s.gff3"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">)</span></span>
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17
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">in_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFF3Writer</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">reader</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse_in_parts</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">,</span> <span class="n" style="color: #333;">target_lines</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">25000</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">__doc__</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#ffc65bbac955d1dfd401d64cad0a8512786eeafd"><strong style="font-weight: bold;">Scripts/gff/gff_to_biosql.py</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Load a fasta file of sequences and associated GFF file into BioSQL.</span></span>
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3
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="python"></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">You will need to adjust the database parameters and have a BioSQL database set</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">up. See:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">http://biopython.org/wiki/BioSQL</span></span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">Depending on the size of the sequences being loaded, you may also get errors on</span></span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">loading very large chromosome sequences. Updating these options can help:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;"> set global max_allowed_packet=1000000000;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;"> set global net_buffer_length=1000000;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;"> gff_to_biosql.py <fasta file> <gff file></span></span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">with_statement</span></span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BioSQL</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BioSeqDatabase</span></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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23
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="python"></span>
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24
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio.GFF</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFFParser</span></span>
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25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">,</span> <span class="n" style="color: #333;">gff_file</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -- To be customized</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># You need to update these parameters to point to your local database</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># XXX demo example could be swapped to use SQLite when that is integrated</span></span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">user</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"chapmanb"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">passwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cdev"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">host</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"localhost"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
33
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">db_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb199_gff"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
34
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">biodb_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb199_gff_cds_pcr"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
35
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># These need to be updated to reflect what you would like to parse</span></span>
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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
36
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># out of the GFF file. Set limit_info=None to parse everything, but</span></span>
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37
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># be sure the file is small or you may deal with memory issues.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
38
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">rnai_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">'Orfeome'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
39
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'GenePair_STS'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
40
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Promoterome'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">)]</span></span>
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41
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">gene_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">'Non_coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
42
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
43
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
44
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
45
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span><span class="n" style="color: #333;">gff_source_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rnai_types</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gene_types</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
46
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># --</span></span>
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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
47
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Parsing FASTA sequence file..."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
48
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">seq_handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
49
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">seq_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
50
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
51
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Parsing GFF data file..."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
52
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
53
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">limit_info</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
54
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
55
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Writing to BioSQL database..."</span></span>
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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
56
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">server</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BioSeqDatabase</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">open_database</span><span class="p">(</span><span class="n" style="color: #333;">driver</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"MySQLdb"</span><span class="p">,</span> <span class="n" style="color: #333;">user</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">user</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
57
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">passwd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">passwd</span><span class="p">,</span> <span class="n" style="color: #333;">host</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">host</span><span class="p">,</span> <span class="n" style="color: #333;">db</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">db_name</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
58
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
59
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">biodb_name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">():</span></span>
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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
60
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">new_database</span><span class="p">(</span><span class="n" style="color: #333;">biodb_name</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
61
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
62
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">remove_database</span><span class="p">(</span><span class="n" style="color: #333;">biodb_name</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
63
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="n" style="color: #333;">adaptor</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">commit</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
64
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">new_database</span><span class="p">(</span><span class="n" style="color: #333;">biodb_name</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
65
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">db</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">server</span><span class="p">[</span><span class="n" style="color: #333;">biodb_name</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
66
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">load</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
67
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="n" style="color: #333;">adaptor</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">commit</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
68
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
69
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="n" style="color: #333;">adaptor</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">rollback</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
70
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
71
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
72
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
74
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">__doc__</span></span>
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75
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
76
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#1f1f2724f86460cdf01eaf8c32d97cf05f74f121"><strong style="font-weight: bold;">Scripts/gff/gff_to_genbank.py</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Convert a GFF and associated FASTA file into GenBank format.</span></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="python"></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> gff_to_genbank.py <GFF annotation file> [<FASTA sequence file> <molecule type>]</span></span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;"> FASTA sequence file: input sequences matching records in GFF. Optional if sequences</span></span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;"> are in the GFF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;"> molecule type: type of molecule in the GFF file. Defaults to DNA, the most common case.</span></span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="python"></span>
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13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="python"></span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>
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19
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">molecule_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"DNA"</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"%s.gb"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fasta_file</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">fasta_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fasta_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">fasta_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">gff_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_input</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">_check_gff</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">_fix_ncbi_id</span><span class="p">(</span><span class="n" style="color: #333;">gff_iter</span><span class="p">),</span> <span class="n" style="color: #333;">molecule_type</span><span class="p">),</span> <span class="n" style="color: #333;">out_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"genbank"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="python"></span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_fix_ncbi_id</span><span class="p">(</span><span class="n" style="color: #333;">fasta_iter</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"""GenBank identifiers can only be 16 characters; try to shorten NCBI.</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta_iter</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
35
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">16</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"|"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
36
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">new_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"|"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
37
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: shortening NCBI name %s to %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">new_id</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
38
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_id</span></span>
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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
39
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_id</span></span>
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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
40
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">rec</span></span>
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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
41
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
42
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
43
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_gff</span><span class="p">(</span><span class="n" style="color: #333;">gff_iterator</span><span class="p">,</span> <span class="n" style="color: #333;">molecule_type</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
44
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check GFF files before feeding to SeqIO to be sure they have sequences.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
45
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
46
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gff_iterator</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
47
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"molecule_type"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
48
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"molecule_type"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">molecule_type</span></span>
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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
49
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="nf" style="color: #900; font-weight: 600;">_flatten_features</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
50
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="python"></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="python"></span>
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52
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_flatten_features</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
53
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"""Make sub_features in an input rec flat for output.</span></span>
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54
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
55
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> GenBank does not handle nested features, so we want to make</span></span>
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56
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> everything top level.</span></span>
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57
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
58
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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59
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">:</span></span>
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60
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">f</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
61
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
62
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">nextf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
63
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">curf</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur</span><span class="p">:</span></span>
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64
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">curf</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
65
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">curf</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
66
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">nextf</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">extend</span><span class="p">(</span><span class="n" style="color: #333;">curf</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
67
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextf</span></span>
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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
68
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out</span></span>
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69
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rec</span></span>
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70
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="python"></span>
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71
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
72
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#0f40c25b1a1324c08d8f7a1cf332d7006641fbca"><strong style="font-weight: bold;">Tests/GFF/F3-unique-3.v2.gff</strong>
deleted</a>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##solid-gff-version 0.2</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">##gff-version 2</span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">##source-version MaToGff.java v1.5</span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">##date 2008-05-28</span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">##time 13:11:03</span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">##Type solid_read</span>
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7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">##color-code AA=0,AC=1,AG=2,AT=3,CA=1,CC=0,CG=3,CT=2,GA=2,GC=3,GG=0,GT=1,TA=3,TC=2,TG=1,TT=0</span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">##primer-base F3=T</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">##max-num-mismatches 3</span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">##max-read-length 20</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">##line-order fragment</span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">##history filter_fasta.pl --noduplicates --output=/data/results/DAEMON/DAEMON_MATE_PAIRS_2_20070326/S1/results.01/primary.20071218094706805 --name=DAEMON_MATE_PAIRS_2_20070326_S1 --tag=F3 --minlength=20 --prefix=T /data/results/DAEMON/DAEMON_MATE_PAIRS_2_20070326/S1/jobs/postPrimerSetPrimary.117/rawseq</span>
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13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">##history map /data/results/RegressionDriver/CaseManager/results/r12/integration/case0002/reads1/test_S1_F3.csfasta /data/results/RegressionDriver/CaseManager/knownData/validatedReference/matchingPipeline/ecoli_k12_MG1655.fasta T=30 L=19 C=1 E=.Tmpfile1211939575SVhDtd F=0 B=1 D=1 u=1 r=0 n=1 Z=1000 P="0000000111111111111" M=0 U=0.000000 H=0 > .Tmpfile1211939575SVhDtd.out.1</span>
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14
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">##history MaToGff.java --sort --qvs=test_S1_F3_QV.qual.txt --convert=unique --clear=3 --tempdir=../tmp test_S1_F3.csfasta.ma.20.3</span>
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15
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103
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="plaintext">3_151_283_F3 solid read 4148264 4148283 9.7 + . g=T3230210232022111220;i=1;p=1.000;q=9,14,6,25,25,19,6,4,16,11,12,20,10,13,26,19,6,4,19,14;u=0,0,1</span>
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114
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115
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116
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117
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118
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119
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120
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121
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122
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123
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125
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126
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127
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC127" class="line" lang="plaintext">3_300_1439_F3 solid read 4580452 4580471 12.3 - . g=A0331111211302100201;i=1;p=1.000;q=5,17,21,14,4,16,11,27,21,9,17,17,27,23,12,21,16,27,25,25;u=0,0,0,1</span>
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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
128
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC128" class="line" lang="plaintext"># Elapsed time 0.846 secs</span></pre></td>
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<li id="455598c9a26aecd6f54c537a558d530222fe275a">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#455598c9a26aecd6f54c537a558d530222fe275a"><strong style="font-weight: bold;">Tests/GFF/c_elegans_WS199_ann_gff.txt</strong>
deleted</a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext"># modified GFF file to remove location coordinates and test annotations</span>
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2
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#fe28203b812c0499b74f4922332eca3744fec114"><strong style="font-weight: bold;">Tests/GFF/c_elegans_WS199_dna_shortened.fa</strong>
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19
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">>MtDNA</span>
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20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="plaintext">cagtaaatagtttaataaaaatatagcatttgggttgctaagatattattactgatagaa</span>
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21
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="plaintext">tttttagtttaatttagaatgtatcacttacaatgatggg</span></pre></td>
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<li id="82717fa145804b249abb52d06924da7668cf62e4">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#82717fa145804b249abb52d06924da7668cf62e4"><strong style="font-weight: bold;">Tests/GFF/c_elegans_WS199_shortened_gff.txt</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">I Orfeome PCR_product 12759747 12764936 . - . amplified=1;pcr_product=mv_B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 12763533 12763553 . - . count=1;gene=amx-2;sequence=SAGE:ggcagagtcttttggca;transcript=B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 12761492 12761512 . - . count=5;gene=amx-2;sequence=SAGE:aacggagccgtacacgc;transcript=B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">I SAGE_tag_most_three_prime SAGE_tag 12761499 12761512 . - . count=9;gene=amx-2;sequence=SAGE:aacggagccg;transcript=B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">X SAGE_tag SAGE_tag 6819353 6819366 . + . count=9;gene=amx-2;sequence=SAGE:aacggagccg;transcript=B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">I Expr_profile experimental_result_region 12762449 12764118 . + . expr_profile=B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">I Coding_transcript CDS 12759745 12759828 . - 0 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">I Coding_transcript CDS 12759949 12760013 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">I Coding_transcript CDS 12760227 12760319 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">I Coding_transcript CDS 12760365 12760494 . - 0 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">I Coding_transcript CDS 12760834 12760904 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">I Coding_transcript CDS 12761172 12761516 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">I Coding_transcript CDS 12761799 12761953 . - 1 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">I Coding_transcript CDS 12762127 12762268 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">I Coding_transcript CDS 12762648 12762806 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">I Coding_transcript CDS 12763112 12763249 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">I Coding_transcript CDS 12763448 12763655 . - 0 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="plaintext">I Coding_transcript CDS 12763729 12763882 . - 1 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">I Coding_transcript CDS 12763979 12764102 . - 2 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="plaintext">I Coding_transcript CDS 12764291 12764471 . - 0 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="plaintext">I Coding_transcript CDS 12764812 12764937 . - 0 ID=CDS:B0019.1;Parent=Transcript:B0019.1;locus=amx-2;status=Partially_confirmed;wormpep=CE:CE40797</span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="plaintext">I history CDS 12759745 12759828 . - 0 ID=CDS:B0019.1:wp173</span>
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23
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="plaintext">I history CDS 12759949 12760013 . - 2 ID=CDS:B0019.1:wp173</span>
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24
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="plaintext">I history CDS 12760227 12760319 . - 2 ID=CDS:B0019.1:wp173</span>
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25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="plaintext">I history CDS 12760365 12760494 . - 0 ID=CDS:B0019.1:wp173</span>
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26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="plaintext">I history CDS 12760834 12760904 . - 2 ID=CDS:B0019.1:wp173</span>
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27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="plaintext">I history CDS 12761172 12761516 . - 2 ID=CDS:B0019.1:wp173</span>
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28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="plaintext">I history CDS 12761577 12761626 . - 1 ID=CDS:B0019.1:wp173</span>
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29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="plaintext">I history CDS 12761795 12761953 . - 1 ID=CDS:B0019.1:wp173</span>
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30
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="plaintext">I history CDS 12762127 12762268 . - 2 ID=CDS:B0019.1:wp173</span>
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31
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="plaintext">I history CDS 12762648 12762806 . - 2 ID=CDS:B0019.1:wp173</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="plaintext">I history CDS 12763112 12763249 . - 2 ID=CDS:B0019.1:wp173</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="plaintext">I history CDS 12763448 12763655 . - 0 ID=CDS:B0019.1:wp173</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC34" class="line" lang="plaintext">I history CDS 12763729 12763882 . - 1 ID=CDS:B0019.1:wp173</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="plaintext">I history CDS 12763979 12764102 . - 2 ID=CDS:B0019.1:wp173</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="plaintext">I history CDS 12764291 12764471 . - 0 ID=CDS:B0019.1:wp173</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="plaintext">I history CDS 12764812 12764937 . - 0 ID=CDS:B0019.1:wp173</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="plaintext">I history CDS 12759745 12759828 . - 0 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="plaintext">I history CDS 12759949 12760013 . - 2 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="plaintext">I history CDS 12760227 12760319 . - 2 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="plaintext">I history CDS 12761172 12761516 . - 2 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="plaintext">I history CDS 12761577 12761626 . - 1 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="plaintext">I history CDS 12761795 12761953 . - 1 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="plaintext">I history CDS 12762127 12762268 . - 2 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="plaintext">I history CDS 12762648 12762806 . - 2 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="plaintext">I history CDS 12763112 12763249 . - 2 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="plaintext">I history CDS 12763469 12763655 . - 0 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="plaintext">I history CDS 12763729 12763882 . - 1 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="plaintext">I history CDS 12763979 12764102 . - 2 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="plaintext">I history CDS 12764291 12764471 . - 0 ID=CDS:B0019.1:wp90</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="plaintext">I history CDS 12764812 12764937 . - 0 ID=CDS:B0019.1:wp90</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12761920 12761953 . - . ID=Target:381130;Target=Mass_spec_peptide:MSP:FADFSPLDVSDVNFATDDLAK 10 21 +;Note=MSP:FADFSPLDVSDVNFATDDLAK;cds_matches=B0019.1;protein_matches=WP:CE40797;times_observed=3</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12762127 12762155 . - . ID=Target:381130;Target=Mass_spec_peptide:MSP:FADFSPLDVSDVNFATDDLAK 1 10 +;Note=MSP:FADFSPLDVSDVNFATDDLAK;cds_matches=B0019.1;protein_matches=WP:CE40797;times_observed=3</span>
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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
54
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12763506 12763559 . - . ID=Target:381133;Target=Mass_spec_peptide:MSP:FGHGQSLLAQGGMNEVVR 1 18 +;Note=MSP:FGHGQSLLAQGGMNEVVR;cds_matches=B0019.1;protein_matches=WP:CE40797;times_observed=1</span>
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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
55
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12764361 12764411 . - . ID=Target:381144;Target=Mass_spec_peptide:MSP:NIQQNRPGLSVLVLEAR 1 17 +;Note=MSP:NIQQNRPGLSVLVLEAR;cds_matches=B0019.1;protein_matches=WP:CE40797;times_observed=2</span>
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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
56
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="plaintext">I Coding_transcript mRNA 12759582 12764949 . - . ID=Transcript:B0019.1;Note=amx-2;Parent=Gene:WBGene00000138;cds=B0019.1;prediction_status=Partially_confirmed;wormpep=CE:CE40797</span>
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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
57
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="plaintext">I Allele SNP 12764272 12764272 . + . interpolated_map_position=14.003;rflp=No;variation=snp_B0019[1]</span>
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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
58
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="plaintext">I Oligo_set reagent 12759745 12761589 . - . oligo_set=Aff_B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
59
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="plaintext">I Coding_transcript exon 12759745 12759828 . - 0 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="60" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
60
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="plaintext">I Coding_transcript exon 12759949 12760013 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
61
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="plaintext">I Coding_transcript exon 12760227 12760319 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
62
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="plaintext">I Coding_transcript exon 12760365 12760494 . - 0 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
63
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="plaintext">I Coding_transcript exon 12760834 12760904 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
64
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="plaintext">I Coding_transcript exon 12761172 12761516 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="65" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
65
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC65" class="line" lang="plaintext">I Coding_transcript exon 12761799 12761953 . - 1 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="66" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
66
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="plaintext">I Coding_transcript exon 12762127 12762268 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
67
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="plaintext">I Coding_transcript exon 12762648 12762806 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
68
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="plaintext">I Coding_transcript exon 12763112 12763249 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
69
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="plaintext">I Coding_transcript exon 12763448 12763655 . - 0 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
70
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="plaintext">I Coding_transcript exon 12763729 12763882 . - 1 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
71
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="plaintext">I Coding_transcript exon 12763979 12764102 . - 2 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
72
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="plaintext">I Coding_transcript exon 12764291 12764471 . - 0 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="plaintext">I Coding_transcript exon 12764812 12764937 . - 0 Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
74
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="plaintext">I Coding_transcript five_prime_UTR 12764938 12764949 . - . Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
75
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC75" class="line" lang="plaintext">I Coding_transcript three_prime_UTR 12759582 12759744 . - . Parent=Transcript:B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
76
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="plaintext">I Coding_transcript intron 12760495 12760833 . - . Parent=Transcript:B0019.1;confirmed_est=EC027594</span>
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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
77
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="plaintext">I Coding_transcript intron 12760905 12761171 . - . Parent=Transcript:B0019.1;confirmed_est=EC027594</span>
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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
78
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC78" class="line" lang="plaintext">I Coding_transcript intron 12761517 12761798 . - . Parent=Transcript:B0019.1;confirmed_est=EC027594</span>
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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
79
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="plaintext">I Coding_transcript intron 12759829 12759948 . - . Parent=Transcript:B0019.1;confirmed_est=EC034652</span>
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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
80
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC80" class="line" lang="plaintext">I Coding_transcript intron 12760014 12760226 . - . Parent=Transcript:B0019.1;confirmed_est=EC034652</span>
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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
81
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="plaintext">I Coding_transcript intron 12760320 12760364 . - . Parent=Transcript:B0019.1;confirmed_est=yk1054h04.3</span>
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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
82
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC82" class="line" lang="plaintext">I Coding_transcript intron 12763883 12763978 . - . Parent=Transcript:B0019.1;confirmed_est=yk1054h04.5,OSTF088D9_1</span>
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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
83
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC83" class="line" lang="plaintext">I Coding_transcript intron 12764103 12764290 . - . Parent=Transcript:B0019.1;confirmed_est=yk1054h04.5,OSTF088D9_1</span>
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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
84
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC84" class="line" lang="plaintext">I Coding_transcript intron 12764472 12764811 . - . Parent=Transcript:B0019.1;confirmed_est=yk1054h04.5,OSTF088D9_1</span>
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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
85
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="plaintext">I Coding_transcript intron 12762807 12763111 . - . Parent=Transcript:B0019.1;confirmed_est=yk1056c07.5</span>
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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
86
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC86" class="line" lang="plaintext">I Coding_transcript intron 12763250 12763447 . - . Parent=Transcript:B0019.1;confirmed_est=yk1056c07.5</span>
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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
87
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="plaintext">I Coding_transcript intron 12763656 12763728 . - . Parent=Transcript:B0019.1;confirmed_est=yk1056c07.5</span>
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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
88
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC88" class="line" lang="plaintext">I Coding_transcript intron 12761954 12762126 . - . Parent=Transcript:B0019.1;confirmed_est=yk262g9.5</span>
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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
89
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC89" class="line" lang="plaintext">I Coding_transcript intron 12762269 12762647 . - . Parent=Transcript:B0019.1;confirmed_est=yk262g9.5</span>
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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
90
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="plaintext">I Promoterome PCR_product 12764938 12766937 . + . pcr_product=p_B0019.1_93</span>
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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
91
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="plaintext">I GenePair_STS PCR_product 12762449 12764118 . + . pcr_product=sjj_B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
92
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC92" class="line" lang="plaintext">I Coding_transcript gene 12759582 12764949 . - . ID=Gene:WBGene00000138</span>
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<td class="old_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
93
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC93" class="line" lang="plaintext">III Orfeome PCR_product 13780230 13780850 . + . amplified=1;pcr_product=mv_3R5.1.v6</span>
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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
94
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC94" class="line" lang="plaintext">IV Orfeome PCR_product 17486939 17488952 . - . amplified=1;pcr_product=mv_4R79.1</span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
95
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC95" class="line" lang="plaintext">IV Orfeome PCR_product 17480353 17483284 . - . amplified=1;pcr_product=mv_4R79.2</span>
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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
96
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC96" class="line" lang="plaintext">X Orfeome PCR_product 17714881 17718531 . + . amplified=1;pcr_product=mv_6R55.1</span>
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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
97
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC97" class="line" lang="plaintext">X Orfeome PCR_product 17712787 17714742 . + . amplified=1;pcr_product=mv_6R55.2</span>
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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
98
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC98" class="line" lang="plaintext">II Orfeome PCR_product 6995874 7010146 . + . amplified=1;pcr_product=mv_AAA03517</span>
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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
99
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC99" class="line" lang="plaintext">III Orfeome PCR_product 5625097 5631795 . + . amplified=1;pcr_product=mv_AAA03544</span>
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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
100
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC100" class="line" lang="plaintext">X GenePair_STS PCR_product 9962853 9963737 . + . pcr_product=cenix:102-c3</span>
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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
101
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC101" class="line" lang="plaintext">II GenePair_STS PCR_product 5507236 5508135 . + . pcr_product=cenix:102-c4</span>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
102
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC102" class="line" lang="plaintext">V GenePair_STS PCR_product 10117842 10118735 . + . pcr_product=cenix:102-c5</span>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
103
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC103" class="line" lang="plaintext">IV GenePair_STS PCR_product 3566130 3567025 . + . pcr_product=cenix:102-c6</span>
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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
104
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC104" class="line" lang="plaintext">X GenePair_STS PCR_product 6117180 6117930 . + . pcr_product=cenix:102-c7</span>
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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
105
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC105" class="line" lang="plaintext">IV GenePair_STS PCR_product 7189492 7190369 . + . pcr_product=cenix:102-c9</span>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
106
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC106" class="line" lang="plaintext">II GenePair_STS PCR_product 14462527 14463202 . + . pcr_product=cenix:102-d1</span>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
107
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC107" class="line" lang="plaintext">X Promoterome PCR_product 2258069 2259336 . + . pcr_product=p_AH9.2_93</span>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
108
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC108" class="line" lang="plaintext">IV Promoterome PCR_product 12157449 12159448 . + . pcr_product=p_B0001.6_93</span>
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<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
109
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC109" class="line" lang="plaintext">I Promoterome PCR_product 12764938 12766937 . + . pcr_product=p_B0019.1_93</span>
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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
110
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC110" class="line" lang="plaintext">V Promoterome PCR_product 10320122 10320689 . + . pcr_product=p_B0024.12_93</span>
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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
111
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC111" class="line" lang="plaintext">I Coding_transcript CDS 4581214 4581237 . - 0 ID=CDS:D1007.5b;Parent=Transcript:D1007.5b.2,Transcript:D1007.5b.1;status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
112
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC112" class="line" lang="plaintext">I Coding_transcript CDS 4581664 4582026 . - 0 ID=CDS:D1007.5b;Parent=Transcript:D1007.5b.2,Transcript:D1007.5b.1;status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
113
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="plaintext">I Coding_transcript CDS 4582412 4582718 . - 1 ID=CDS:D1007.5b;Parent=Transcript:D1007.5b.2,Transcript:D1007.5b.1;status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
114
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC114" class="line" lang="plaintext">I Coding_transcript CDS 4583190 4583374 . - 0 ID=CDS:D1007.5b;Parent=Transcript:D1007.5b.2,Transcript:D1007.5b.1;status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
115
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC115" class="line" lang="plaintext">I Coding_transcript CDS 4583426 4583509 . - 0 ID=CDS:D1007.5b;Parent=Transcript:D1007.5b.2,Transcript:D1007.5b.1;status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
116
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC116" class="line" lang="plaintext">I Coding_transcript CDS 4583560 4583805 . - 0 ID=CDS:D1007.5b;Parent=Transcript:D1007.5b.2,Transcript:D1007.5b.1;status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
117
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC117" class="line" lang="plaintext">I Coding_transcript mRNA 4580734 4583815 . - . ID=Transcript:D1007.5b.1;Parent=Gene:WBGene00017003;cds=D1007.5b;prediction_status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
118
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC118" class="line" lang="plaintext">I Coding_transcript mRNA 4581214 4583811 . - . ID=Transcript:D1007.5b.2;Parent=Gene:WBGene00017003;cds=D1007.5b;prediction_status=Confirmed;wormpep=WP:CE33577</span>
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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
119
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC119" class="line" lang="plaintext">I Coding_transcript exon 4581214 4581237 . - 0 Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
120
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC120" class="line" lang="plaintext">I Coding_transcript exon 4581664 4582026 . - 0 Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
121
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC121" class="line" lang="plaintext">I Coding_transcript exon 4582412 4582718 . - 1 Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
122
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC122" class="line" lang="plaintext">I Coding_transcript exon 4583190 4583374 . - 0 Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
123
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC123" class="line" lang="plaintext">I Coding_transcript exon 4583426 4583509 . - 0 Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
124
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC124" class="line" lang="plaintext">I Coding_transcript exon 4583560 4583805 . - 0 Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
125
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC125" class="line" lang="plaintext">I Coding_transcript five_prime_UTR 4583806 4583815 . - . Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
126
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC126" class="line" lang="plaintext">I Coding_transcript three_prime_UTR 4580734 4581213 . - . Parent=Transcript:D1007.5b.1</span>
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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
127
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC127" class="line" lang="plaintext">I Coding_transcript intron 4582027 4582411 . - . Parent=Transcript:D1007.5b.1;confirmed_est=EB994038</span>
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128
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC128" class="line" lang="plaintext">I Coding_transcript intron 4583375 4583425 . - . Parent=Transcript:D1007.5b.1;confirmed_est=EC038345,OSTF085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
129
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC129" class="line" lang="plaintext">I Coding_transcript intron 4583510 4583559 . - . Parent=Transcript:D1007.5b.1;confirmed_est=EC038345,OSTF085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
130
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC130" class="line" lang="plaintext">I Coding_transcript intron 4582719 4583189 . - . Parent=Transcript:D1007.5b.1;confirmed_est=yk1055g06.5,OSTF085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
131
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC131" class="line" lang="plaintext">I Coding_transcript intron 4581238 4581663 . - . Parent=Transcript:D1007.5b.1;confirmed_est=yk1057e08.3</span>
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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
132
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC132" class="line" lang="plaintext">I Coding_transcript exon 4581214 4581237 . - 0 Parent=Transcript:D1007.5b.2</span>
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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
133
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC133" class="line" lang="plaintext">I Coding_transcript exon 4581664 4582026 . - 0 Parent=Transcript:D1007.5b.2</span>
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<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
134
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC134" class="line" lang="plaintext">I Coding_transcript exon 4582412 4582718 . - 1 Parent=Transcript:D1007.5b.2</span>
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<td class="old_line diff-line-num old" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
135
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC135" class="line" lang="plaintext">I Coding_transcript exon 4583190 4583374 . - 0 Parent=Transcript:D1007.5b.2</span>
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<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
136
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC136" class="line" lang="plaintext">I Coding_transcript exon 4583426 4583509 . - 0 Parent=Transcript:D1007.5b.2</span>
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<td class="old_line diff-line-num old" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
137
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC137" class="line" lang="plaintext">I Coding_transcript exon 4583560 4583805 . - 0 Parent=Transcript:D1007.5b.2</span>
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<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
138
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC138" class="line" lang="plaintext">I Coding_transcript five_prime_UTR 4583806 4583811 . - . Parent=Transcript:D1007.5b.2</span>
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<td class="old_line diff-line-num old" data-linenumber="139" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
139
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC139" class="line" lang="plaintext">I Coding_transcript intron 4582027 4582411 . - . Parent=Transcript:D1007.5b.2;confirmed_est=EB994038</span>
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<td class="old_line diff-line-num old" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
140
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC140" class="line" lang="plaintext">I Coding_transcript intron 4583375 4583425 . - . Parent=Transcript:D1007.5b.2;confirmed_est=EC038345,OSTF085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
141
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC141" class="line" lang="plaintext">I Coding_transcript intron 4583510 4583559 . - . Parent=Transcript:D1007.5b.2;confirmed_est=EC038345,OSTF085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
142
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC142" class="line" lang="plaintext">I Coding_transcript intron 4582719 4583189 . - . Parent=Transcript:D1007.5b.2;confirmed_est=yk1055g06.5,OSTF085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
143
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC143" class="line" lang="plaintext">I Coding_transcript intron 4581238 4581663 . - . Parent=Transcript:D1007.5b.2;confirmed_est=yk1057e08.3</span>
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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
144
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC144" class="line" lang="plaintext">I Coding_transcript gene 4580693 4583815 . - . ID=Gene:WBGene00017003</span>
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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
145
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC145" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4581093 4581113 . - . count=10;gene=D1007.5;sequence=SAGE:tttgcgaattacttgct;transcript=D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
146
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC146" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4580748 4580768 . - . count=112;gene=D1007.5;sequence=SAGE:ttttccattaattttga;transcript=D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
147
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC147" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4582415 4582428 . - . count=1;gene=D1007.5;sequence=SAGE:cattttcgtg;transcript=D1007.5b.2,D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
148
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC148" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4580914 4580927 . - . count=1;gene=D1007.5;sequence=SAGE:taaatttcaa;transcript=D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
149
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC149" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4581193 4581206 . - . count=1;gene=D1007.5;sequence=SAGE:tgctcgttcg;transcript=D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
150
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC150" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4583465 4583478 . - . count=1;gene=D1007.5;sequence=SAGE:tgttggcctt;transcript=D1007.5b.2,D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
151
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC151" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4583458 4583478 . - . count=1;gene=D1007.5;sequence=SAGE:tgttggccttttacttg;transcript=D1007.5b.2,D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
152
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC152" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4582533 4582553 . - . count=2;gene=D1007.5;sequence=SAGE:tgcagtgatagtccagc;transcript=D1007.5b.2,D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
153
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC153" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4581100 4581113 . - . count=2;gene=D1007.5;sequence=SAGE:tttgcgaatt;transcript=D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
154
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC154" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 4580755 4580768 . - . count=43;gene=D1007.5;sequence=SAGE:ttttccatta;transcript=D1007.5b.1,D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
155
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC155" class="line" lang="plaintext">I Coding_transcript CDS 4580993 4581241 . - 0 ID=CDS:D1007.5a;Parent=Transcript:D1007.5a;status=Confirmed;wormpep=CE:CE29034</span>
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<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
156
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC156" class="line" lang="plaintext">I Coding_transcript CDS 4581664 4582026 . - 0 ID=CDS:D1007.5a;Parent=Transcript:D1007.5a;status=Confirmed;wormpep=CE:CE29034</span>
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<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
157
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC157" class="line" lang="plaintext">I Coding_transcript CDS 4582412 4582718 . - 1 ID=CDS:D1007.5a;Parent=Transcript:D1007.5a;status=Confirmed;wormpep=CE:CE29034</span>
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<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
158
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC158" class="line" lang="plaintext">I Coding_transcript CDS 4583190 4583374 . - 0 ID=CDS:D1007.5a;Parent=Transcript:D1007.5a;status=Confirmed;wormpep=CE:CE29034</span>
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<td class="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
159
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC159" class="line" lang="plaintext">I Coding_transcript CDS 4583426 4583509 . - 0 ID=CDS:D1007.5a;Parent=Transcript:D1007.5a;status=Confirmed;wormpep=CE:CE29034</span>
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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
160
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC160" class="line" lang="plaintext">I Coding_transcript CDS 4583560 4583805 . - 0 ID=CDS:D1007.5a;Parent=Transcript:D1007.5a;status=Confirmed;wormpep=CE:CE29034</span>
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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
161
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC161" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 4580996 4581052 . - . ID=Target:277116;Target=Mass_spec_peptide:MSP:IYEPSQEDLLLMHQLQQER 1 19 +;Note=MSP:IYEPSQEDLLLMHQLQQER;cds_matches=D1007.5a;protein_matches=WP:CE29034;times_observed=1</span>
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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
162
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC162" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 4581838 4581882 . - . ID=Target:277138;Target=Mass_spec_peptide:MSP:AAIHLGSWHQIEGPR 1 15 +;Note=MSP:AAIHLGSWHQIEGPR;cds_matches=D1007.5b D1007.5a;protein_matches=WP:CE33577 WP:CE29034;times_observed=1</span>
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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
163
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC163" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 4583581 4583601 . - . ID=Target:277176;Target=Mass_spec_peptide:MSP:TLWWLPK 1 7 +;Note=MSP:TLWWLPK;cds_matches=D1007.5b D1007.5a;protein_matches=WP:CE33577 WP:CE29034;times_observed=1</span>
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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
164
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC164" class="line" lang="plaintext">I Coding_transcript mRNA 4580693 4583811 . - . ID=Transcript:D1007.5a;Parent=Gene:WBGene00017003;cds=D1007.5a;prediction_status=Confirmed;wormpep=CE:CE29034</span>
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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
165
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC165" class="line" lang="plaintext">I Coding_transcript exon 4580993 4581241 . - 0 Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
166
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC166" class="line" lang="plaintext">I Coding_transcript exon 4581664 4582026 . - 0 Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
167
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC167" class="line" lang="plaintext">I Coding_transcript exon 4582412 4582718 . - 1 Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
168
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC168" class="line" lang="plaintext">I Coding_transcript exon 4583190 4583374 . - 0 Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
169
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC169" class="line" lang="plaintext">I Coding_transcript exon 4583426 4583509 . - 0 Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
170
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC170" class="line" lang="plaintext">I Coding_transcript exon 4583560 4583805 . - 0 Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
171
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC171" class="line" lang="plaintext">I Coding_transcript five_prime_UTR 4583806 4583811 . - . Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
172
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC172" class="line" lang="plaintext">I Coding_transcript three_prime_UTR 4580693 4580992 . - . Parent=Transcript:D1007.5a</span>
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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
173
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC173" class="line" lang="plaintext">I Coding_transcript intron 4582027 4582411 . - . Parent=Transcript:D1007.5a;confirmed_est=EB994038</span>
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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
174
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC174" class="line" lang="plaintext">I Coding_transcript intron 4581242 4581663 . - . Parent=Transcript:D1007.5a;confirmed_est=EB994038,OSTR085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
175
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC175" class="line" lang="plaintext">I Coding_transcript intron 4583375 4583425 . - . Parent=Transcript:D1007.5a;confirmed_est=EC038345,OSTF085G5_1</span>
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176
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC176" class="line" lang="plaintext">I Coding_transcript intron 4583510 4583559 . - . Parent=Transcript:D1007.5a;confirmed_est=EC038345,OSTF085G5_1</span>
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<td class="old_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
177
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC177" class="line" lang="plaintext">I Coding_transcript intron 4582719 4583189 . - . Parent=Transcript:D1007.5a;confirmed_est=yk1055g06.5,OSTF085G5_1</span></pre></td>
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<br>
</li>
<li id="39e312c030efe5a4955659d6cce831c39973fe1f">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#39e312c030efe5a4955659d6cce831c39973fe1f"><strong style="font-weight: bold;">Tests/GFF/ensembl_gtf.txt</strong>
deleted</a>
<hr style="overflow: hidden; border: 1px solid #e1e1e1;">
<table class="code white" style="border-spacing: 0; border-collapse: collapse; width: auto; font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">I snoRNA exon 3747 3909 . - . gene_id "Y74C9A.6"; transcript_id "Y74C9A.6"; exon_number "1"; gene_name "Y74C9A.6"; transcript_name "NR_001477.2";</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">I protein_coding exon 12764812 12764949 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "1"; gene_name "amx-2"; transcript_name "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">I protein_coding CDS 12764812 12764937 . - 0 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "1"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">I protein_coding start_codon 12764935 12764937 . - 0 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "1"; gene_name "amx-2"; transcript_name "B0019.1";</span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">I protein_coding exon 12764291 12764471 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "2"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">I protein_coding CDS 12764291 12764471 . - 0 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "2"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">I protein_coding exon 12763979 12764102 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "3"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">I protein_coding CDS 12763979 12764102 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "3"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">I protein_coding exon 12763729 12763882 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "4"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">I protein_coding CDS 12763729 12763882 . - 1 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "4"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">I protein_coding exon 12763448 12763655 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "5"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">I protein_coding CDS 12763448 12763655 . - 0 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "5"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">I protein_coding exon 12763112 12763249 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "6"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">I protein_coding CDS 12763112 12763249 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "6"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">I protein_coding exon 12762648 12762806 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "7"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">I protein_coding CDS 12762648 12762806 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "7"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">I protein_coding exon 12762127 12762268 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "8"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
</tr>
<tr class="line_holder old" style="line-height: 1.6;">
<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="plaintext">I protein_coding CDS 12762127 12762268 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "8"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">I protein_coding exon 12761799 12761953 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "9"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="plaintext">I protein_coding CDS 12761799 12761953 . - 1 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "9"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="plaintext">I protein_coding exon 12761172 12761516 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "10"; gene_name "amx-2"; transcript_name "B0019.1";</span>
</pre></td>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="plaintext">I protein_coding CDS 12761172 12761516 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "10"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
</pre></td>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="plaintext">I protein_coding exon 12760834 12760904 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "11"; gene_name "amx-2"; transcript_name "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="plaintext">I protein_coding CDS 12760834 12760904 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "11"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="plaintext">I protein_coding exon 12760365 12760494 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "12"; gene_name "amx-2"; transcript_name "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="plaintext">I protein_coding CDS 12760365 12760494 . - 0 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "12"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="plaintext">I protein_coding exon 12760227 12760319 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "13"; gene_name "amx-2"; transcript_name "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="plaintext">I protein_coding CDS 12760227 12760319 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "13"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="plaintext">I protein_coding exon 12759949 12760013 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "14"; gene_name "amx-2"; transcript_name "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="plaintext">I protein_coding CDS 12759949 12760013 . - 2 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "14"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="plaintext">I protein_coding exon 12759579 12759828 . - . gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "15"; gene_name "amx-2"; transcript_name "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="plaintext">I protein_coding CDS 12759748 12759828 . - 0 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "15"; gene_name "amx-2"; transcript_name "B0019.1"; protein_id "B0019.1";</span>
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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
33
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="plaintext">I protein_coding stop_codon 12759745 12759747 . - 0 gene_id "B0019.1"; transcript_id "B0019.1"; exon_number "15"; gene_name "amx-2"; transcript_name "B0019.1";</span></pre></td>
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<li id="baeab9a85d51d35425482edf0e78b2c50bea1824">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#baeab9a85d51d35425482edf0e78b2c50bea1824"><strong style="font-weight: bold;">Tests/GFF/glimmer_nokeyval.gff3</strong>
deleted</a>
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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">##sequence-region scaffold4215_3 1 6526</span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">scaffold4215_3 glimmer gene 3 62 . - . ID=GL0000006;Name=GL0000006;Lack 3'-end;</span>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">scaffold4215_3 glimmer mRNA 3 62 . - . ID=GL0000006;Name=GL0000006;Parent=GL0000006;Lack 3'-end;</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">scaffold4215_3 glimmer CDS 3 62 2.84 - 0 Parent=GL0000006;Lack 3'-end;</span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">scaffold4215_3 glimmer gene 124 1983 . - . ID=GL0000007;Name=GL0000007;Complete;</span></pre></td>
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<li id="e433c519d4214d8282d31ee25c725c2fe46dfd9b">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#e433c519d4214d8282d31ee25c725c2fe46dfd9b"><strong style="font-weight: bold;">Tests/GFF/hybrid1.gff3</strong>
deleted</a>
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1
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">##sequence-region foo 1 100</span>
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3
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">##feature-ontology bar</span>
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4
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">##attribute-ontology baz</span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">##source-ontology boo</span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">##sequence-region chr17 62467934 62469545 </span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">chr17 UCSC mRNA 62467934 62469545 . - . ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:SOMA_HUMAN;Note=growth%20hormone%201;Alias=GH1</span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">chr17 UCSC CDS 62468039 62468236 . - 1 Parent=A00469</span>
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9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">chr17 UCSC CDS 62468490 62468654 . - 2 Parent=A00469</span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">chr17 UCSC CDS 62468747 62468866 . - 1 Parent=A00469</span>
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11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">chr17 UCSC CDS 62469076 62469236 . - 1 Parent=A00469</span>
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12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">chr17 UCSC CDS 62469497 62469506 . - 0 Parent=A00469</span>
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13
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">###</span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">##FASTA</span>
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15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">>chr17</span>
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16
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">GATTACA</span>
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17
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">GATTACA</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#2598951dd9ce972e3fb974dd1069ecb0ac43f16b"><strong style="font-weight: bold;">Tests/GFF/hybrid2.fa</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">>lcl|chr17</span>
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2
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">GATTACA</span>
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3
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">GATTACA</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#162c3679ebe63ccaacf9c1837a27f907a63c61a3"><strong style="font-weight: bold;">Tests/GFF/hybrid2.gff3</strong>
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1
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">##sequence-region foo 1 100</span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">##feature-ontology bar</span>
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4
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">##attribute-ontology baz</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">##source-ontology boo</span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">##sequence-region chr17 62467934 62469545 </span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">chr17 UCSC mRNA 62467934 62469545 . - . ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:SOMA_HUMAN;Note=growth%20hormone%201;Alias=GH1</span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">chr17 UCSC CDS 62468039 62468236 . - 1 Parent=A00469</span>
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9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">chr17 UCSC CDS 62468490 62468654 . - 2 Parent=A00469</span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">chr17 UCSC CDS 62468747 62468866 . - 1 Parent=A00469</span>
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11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">chr17 UCSC CDS 62469076 62469236 . - 1 Parent=A00469</span>
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12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">chr17 UCSC CDS 62469497 62469506 . - 0 Parent=A00469</span>
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13
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">###</span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">##FASTA</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">>lcl|chr17</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">GATTACA</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">GATTACA</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#595e6a53853ddb03fefccd0c05a294b9ed7d2d83"><strong style="font-weight: bold;">Tests/GFF/jgi_gff2.txt</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">chr_1 JGI exon 37061 37174 . - . name "fgenesh1_pg.C_chr_1000007"; transcriptId 873</span>
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2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">chr_1 JGI CDS 37061 37174 . - 0 name "fgenesh1_pg.C_chr_1000007"; proteinId 873; exonNumber 3</span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">chr_1 JGI exon 37315 37620 . - . name "fgenesh1_pg.C_chr_1000007"; transcriptId 873</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">chr_1 JGI CDS 37315 37620 . - 0 name "fgenesh1_pg.C_chr_1000007"; proteinId 873; exonNumber 2</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">chr_1 JGI exon 37752 38216 . - . name "fgenesh1_pg.C_chr_1000007"; transcriptId 873</span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">chr_1 JGI CDS 37752 38216 . - 0 name "fgenesh1_pg.C_chr_1000007"; proteinId 873; exonNumber 1</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#69ca99a2972dee23c74045eb96a2fd7f9959cf55"><strong style="font-weight: bold;">Tests/GFF/mouse_extra_comma.gff3</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">chr17 RefSeq gene 6797760 6818159 . + . ID=NC_000083.5:LOC100040603;Name=NC_000083.5:LOC100040603</span>
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2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">chr17 RefSeq mRNA 6797760 6818159 . + . ID=XM_001475631.1;Parent=NC_000083.5:LOC100040603</span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">chr17 RefSeq protein 6806527 6812289 . + . ID=;Parent=XM_001475631.1</span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">chr17 RefSeq five_prime_UTR 6797760 6797769 . + . Parent=XM_001475631.1</span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">chr17 RefSeq five_prime_UTR 6806513 6806526 . + . Parent=XM_001475631.1</span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">chr17 RefSeq CDS 6806527 6806553 . + 0 Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>
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7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">chr17 RefSeq CDS 6808204 6808245 . + 0 Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">chr17 RefSeq CDS 6811330 6811453 . + 0 Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">chr17 RefSeq CDS 6811792 6811869 . + 2 Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">chr17 RefSeq CDS 6812219 6812289 . + 2 Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">chr17 RefSeq three_prime_UTR 6812290 6818159 . + . Parent=XM_001475631.1</span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">chr17 RefSeq exon 6797760 6797769 . + . Parent=XM_001475631.1</span>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">chr17 RefSeq exon 6806513 6806553 . + . Parent=XM_001475631.1</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">chr17 RefSeq exon 6808204 6808245 . + . Parent=XM_001475631.1</span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">chr17 RefSeq exon 6811330 6811453 . + . Parent=XM_001475631.1</span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">chr17 RefSeq exon 6811792 6811869 . + . Parent=XM_001475631.1</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">chr17 RefSeq exon 6812219 6818159 . + . Parent=XM_001475631.1</span></pre></td>
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<li id="284adb09db73557c24d311d7a9916b60e0a5a809">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#284adb09db73557c24d311d7a9916b60e0a5a809"><strong style="font-weight: bold;">Tests/GFF/ncbi_gff3.txt</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">##source-version NCBI C++ formatter 0.2</span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">##date 2009-04-25</span>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">##Type DNA NC_008596.1</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">NC_008596.1 RefSeq gene 12272 13301 . + . locus_tag=MSMEG_0013;note=ferric%20enterobactin%20transport%20system%20permease%20protein%20FepG%3B%20this%20gene%20contains%20a%20frame%20shift%20which%20is%20not%20the%20result%20of%20sequencing%20error%3B%20identified%20by%20match%20to%20protein%20family%20HMM%20PF01032;pseudo=;db_xref=GeneID:4537201</span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">NC_008596.1 RefSeq gene 1137579 1138550 . + . ID=NC_008596.1:speB;locus_tag=MSMEG_1072;db_xref=GeneID:4535378</span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">NC_008596.1 RefSeq CDS 1137579 1138547 . + 0 ID=NC_008596.1:speB:unknown_transcript_1;Parent=NC_008596.1:speB;locus_tag=MSMEG_1072;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_885468.1;db_xref=GI:118469242;db_xref=GeneID:4535378;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">NC_008596.1 RefSeq start_codon 1137579 1137581 . + 0 ID=NC_008596.1:speB:unknown_transcript_1;Parent=NC_008596.1:speB;locus_tag=MSMEG_1072;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_885468.1;db_xref=GI:118469242;db_xref=GeneID:4535378;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">NC_008596.1 RefSeq stop_codon 1138548 1138550 . + 0 ID=NC_008596.1:speB:unknown_transcript_1;Parent=NC_008596.1:speB;locus_tag=MSMEG_1072;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_885468.1;db_xref=GI:118469242;db_xref=GeneID:4535378;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">NC_008596.1 RefSeq gene 3597069 3598112 . + . ID=NC_008596.1:speB;locus_tag=MSMEG_3535;db_xref=GeneID:4533678</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">NC_008596.1 RefSeq CDS 3597069 3598109 . + 0 ID=NC_008596.1:speB:unknown_transcript_2;Parent=NC_008596.1:speB;locus_tag=MSMEG_3535;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_887838.1;db_xref=GI:118470943;db_xref=GeneID:4533678;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">NC_008596.1 RefSeq start_codon 3597069 3597071 . + 0 ID=NC_008596.1:speB:unknown_transcript_2;Parent=NC_008596.1:speB;locus_tag=MSMEG_3535;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_887838.1;db_xref=GI:118470943;db_xref=GeneID:4533678;exon_number=1</span>
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13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">NC_008596.1 RefSeq stop_codon 3598110 3598112 . + 0 ID=NC_008596.1:speB:unknown_transcript_2;Parent=NC_008596.1:speB;locus_tag=MSMEG_3535;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_887838.1;db_xref=GI:118470943;db_xref=GeneID:4533678;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">NC_008596.1 RefSeq gene 4460713 4461672 . - . ID=NC_008596.1:speB;locus_tag=MSMEG_4374;db_xref=GeneID:4535424</span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">NC_008596.1 RefSeq CDS 4460716 4461672 . - 0 ID=NC_008596.1:speB:unknown_transcript_3;Parent=NC_008596.1:speB;locus_tag=MSMEG_4374;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_888649.1;db_xref=GI:118469662;db_xref=GeneID:4535424;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">NC_008596.1 RefSeq start_codon 4461670 4461672 . - 0 ID=NC_008596.1:speB:unknown_transcript_3;Parent=NC_008596.1:speB;locus_tag=MSMEG_4374;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_888649.1;db_xref=GI:118469662;db_xref=GeneID:4535424;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">NC_008596.1 RefSeq stop_codon 4460713 4460715 . - 0 ID=NC_008596.1:speB:unknown_transcript_3;Parent=NC_008596.1:speB;locus_tag=MSMEG_4374;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_888649.1;db_xref=GI:118469662;db_xref=GeneID:4535424;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="plaintext">NC_008596.1 RefSeq gene 4539385 4540344 . + . ID=NC_008596.1:speB;locus_tag=MSMEG_4459;db_xref=GeneID:4537057</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">NC_008596.1 RefSeq CDS 4539385 4540341 . + 0 ID=NC_008596.1:speB:unknown_transcript_4;Parent=NC_008596.1:speB;locus_tag=MSMEG_4459;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_888732.1;db_xref=GI:118472833;db_xref=GeneID:4537057;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="plaintext">NC_008596.1 RefSeq start_codon 4539385 4539387 . + 0 ID=NC_008596.1:speB:unknown_transcript_4;Parent=NC_008596.1:speB;locus_tag=MSMEG_4459;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_888732.1;db_xref=GI:118472833;db_xref=GeneID:4537057;exon_number=1</span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="plaintext">NC_008596.1 RefSeq stop_codon 4540342 4540344 . + 0 ID=NC_008596.1:speB:unknown_transcript_4;Parent=NC_008596.1:speB;locus_tag=MSMEG_4459;EC_number=3.5.3.11;note=identified%20by%20match%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20protein%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;protein_id=YP_888732.1;db_xref=GI:118472833;db_xref=GeneID:4537057;exon_number=1</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#29db11f1f11aaaca59fe32a3ff3453b37254497b"><strong style="font-weight: bold;">Tests/GFF/problem_sequence_region.gff3</strong>
deleted</a>
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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">#!gff-spec-version 1.21</span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">#!processor NCBI annotwriter</span>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">##sequence-region 1 2482535</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1282</span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">1 Local region 1 2482535 . + . ID=1:1..2482535;Dbxref=taxon:1282;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA</span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">1 . gene 1 1356 . + . ID=gene-test_000001;Name=dnaA;gbkey=Gene;gene=dnaA;gene_biotype=protein_coding</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#b9e1aa3c398e2345520376b31a5cb2096bef8dba"><strong style="font-weight: bold;">Tests/GFF/spaces.gff3</strong>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">contig1 . gene 1544 2057 . - . ID=contig1.1</span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">contig1 . mRNA 1544 2057 . - . ID=mRNA.contig1.1;Parent=contig1.1 </span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">contig1 . mRNA 1544 2057 . - . foo=bar;ID=mRNA.contig1.1;Parent=contig1.1 </span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">contig1 . mRNA 1544 2057 . - . ID=mRNA.contig1.1;Parent=contig1.1; foo=bar</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#5b5a49f848dceb982e0f0b9221513c0367d4a001"><strong style="font-weight: bold;">Tests/GFF/trans_splicing.gff3</strong>
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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">1 manual gene 9559 9672 . + . ID=gene83;Name=rps12|lcl|NC_021456.1_cdsid_YP_008082803.1_8-gene;exception=trans-splicing</span>
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2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">1 manual gene 112442 113241 . + . ID=gene84;Name=rps12|lcl|NC_021456.1_cdsid_YP_008082803.1_8-gene;exception=trans-splicing</span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">1 manual mRNA 9559 9672 . + . ID=mRNA43;Parent=gene83,gene84;Name=rps12|lcl|NC_021456.1_cdsid_YP_008082803.1_8;exception=trans-splicing</span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">1 manual mRNA 112442 113241 . + . ID=mRNA43;Parent=gene83,gene84;Name=rps12|lcl|NC_021456.1_cdsid_YP_008082803.1_8;exception=trans-splicing</span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">1 manual exon 9559 9672 . + . Parent=mRNA43</span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">1 manual CDS 9559 9672 . + 0 Parent=mRNA43</span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">1 manual exon 112442 112673 . + . Parent=mRNA43</span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">1 manual CDS 112442 112673 . + 0 Parent=mRNA43</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">1 manual intron 112674 113215 . + . Parent=mRNA43</span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">1 manual exon 113216 113241 . + . Parent=mRNA43</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">1 manual CDS 113216 113241 . + 2 Parent=mRNA43</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#6c671f0bd5a210f7a94e0c4bab6fd5c1e6068025"><strong style="font-weight: bold;">Tests/GFF/transcripts.gff3</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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2
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">##date 2013-11-13</span>
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3
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">edit_test.fa . gene 500 2610 . + . ID=newGene</span>
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4
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">edit_test.fa . mRNA 500 2385 . + . Parent=newGene;Namo=reinhard+did+this;Name=t1%28newGene%29;ID=t1;uri=http%3A//www.yahoo.com</span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">edit_test.fa . five_prime_UTR 500 802 . + . Parent=t1</span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">edit_test.fa . CDS 803 1012 . + . Parent=t1</span>
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7
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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10
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">edit_test.fa . three_prime_UTR 2047 2385 . + . Parent=t1</span>
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11
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">edit_test.fa . mRNA 1050 2610 . + . Parent=newGene;Name=t2%28newGene%29;ID=t2</span>
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12
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">edit_test.fa . CDS 1050 1196 . + . Parent=t2</span>
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13
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">edit_test.fa . CDS 1472 1651 . + . Parent=t2</span>
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14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">edit_test.fa . CDS 1732 2610 . + . Parent=t2</span>
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15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">edit_test.fa . mRNA 1050 2610 . + . Parent=newGene;Name=t3%28newGene%29;ID=t3</span>
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16
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17
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18
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="plaintext">edit_test.fa . CDS 1732 2610 . + . Parent=t3</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#f4023d8db326a19aa73f1e08c79ba89f9c8ec4ee"><strong style="font-weight: bold;">Tests/GFF/unescaped-semicolon.gff3</strong>
deleted</a>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">chr1 . gene 1 100 . + . ID=PH01000020G1780;Description="osFTL6 FT-Like6 homologous to Flowering Locus T gene; contains Pfam profile PF01161: Phosphatidylethanolamine-binding protein, expressed"</span></pre></td>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#dc72ce464baa5740ce7acbbe1c08bab5e1dc1039"><strong style="font-weight: bold;">Tests/GFF/wormbase_gff2.txt</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">I Genomic_canonical region 1 2679 . + . Sequence "cTel33B" ; Note "Clone cTel33B; Genbank AC199162" ; Note "Clone cTel33B; Genbank AC199162"</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">I Coding_transcript Transcript 12759582 12764949 . - . Transcript "B0019.1" ; WormPep "WP:CE40797" ; Note "amx-2" ; Prediction_status "Partially_confirmed" ; Gene "WBGene00000138" ; CDS "B0019.1" ; WormPep "WP:CE40797" ; Note "amx-2" ; Prediction_status "Partially_confirmed" ; Gene "WBGene00000138"</span>
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<td class="old_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">I Coding_transcript intron 12759829 12759948 . - . Transcript "B0019.1" ; Confirmed_EST EC034652</span>
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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">I Coding_transcript intron 12760014 12760226 . - . Transcript "B0019.1" ; Confirmed_EST EC034652</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">I Coding_transcript intron 12760320 12760364 . - . Transcript "B0019.1" ; Confirmed_EST yk1054h04.3</span>
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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">I Coding_transcript intron 12760495 12760833 . - . Transcript "B0019.1" ; Confirmed_EST EC027594</span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">I Coding_transcript intron 12760905 12761171 . - . Transcript "B0019.1" ; Confirmed_EST EC027594</span>
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<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">I Coding_transcript intron 12761517 12761798 . - . Transcript "B0019.1" ; Confirmed_EST EC027594</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">I Coding_transcript intron 12761954 12762126 . - . Transcript "B0019.1" ; Confirmed_EST yk262g9.5</span>
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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">I Coding_transcript intron 12762269 12762647 . - . Transcript "B0019.1" ; Confirmed_EST yk262g9.5</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">I Coding_transcript intron 12762807 12763111 . - . Transcript "B0019.1" ; Confirmed_EST yk1056c07.5</span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">I Coding_transcript intron 12763250 12763447 . - . Transcript "B0019.1" ; Confirmed_EST yk1056c07.5</span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">I Coding_transcript intron 12763656 12763728 . - . Transcript "B0019.1" ; Confirmed_EST yk1056c07.5</span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">I Coding_transcript intron 12763883 12763978 . - . Transcript "B0019.1" ; Confirmed_EST yk1054h04.5 ; Confirmed_EST OSTF088D9_1</span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">I Coding_transcript intron 12764103 12764290 . - . Transcript "B0019.1" ; Confirmed_EST yk1054h04.5 ; Confirmed_EST OSTF088D9_1</span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">I Coding_transcript intron 12764472 12764811 . - . Transcript "B0019.1" ; Confirmed_EST yk1054h04.5 ; Confirmed_EST OSTF088D9_1</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">I Coding_transcript exon 12759582 12759828 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="plaintext">I Coding_transcript exon 12759949 12760013 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="plaintext">I Coding_transcript exon 12760227 12760319 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="plaintext">I Coding_transcript exon 12760365 12760494 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
21
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="plaintext">I Coding_transcript exon 12760834 12760904 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
22
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="plaintext">I Coding_transcript exon 12761172 12761516 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="plaintext">I Coding_transcript exon 12761799 12761953 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="plaintext">I Coding_transcript exon 12762127 12762268 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="plaintext">I Coding_transcript exon 12762648 12762806 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="plaintext">I Coding_transcript exon 12763112 12763249 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="plaintext">I Coding_transcript exon 12763448 12763655 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="plaintext">I Coding_transcript exon 12763729 12763882 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="plaintext">I Coding_transcript exon 12763979 12764102 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="plaintext">I Coding_transcript exon 12764291 12764471 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="plaintext">I Coding_transcript exon 12764812 12764949 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 12761492 12761512 . - . Sequence SAGE:aacggagccgtacacgc;count 5;Gene amx-2;Transcript B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
33
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="plaintext">I SAGE_tag_most_three_prime SAGE_tag 12761499 12761512 . - . Sequence SAGE:aacggagccg;count 9;Gene amx-2;Transcript B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
34
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC34" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12761920 12761953 . - . Target "Mass_spec_peptide:MSP:FADFSPLDVSDVNFATDDLAK" 10 21 ; Note "MSP:FADFSPLDVSDVNFATDDLAK" ; Protein_matches "WP:CE40797" ; CDS_matches "B0019.1" ; Times_observed "3"</span>
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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
35
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12762127 12762155 . - . Target "Mass_spec_peptide:MSP:FADFSPLDVSDVNFATDDLAK" 1 10 ; Note "MSP:FADFSPLDVSDVNFATDDLAK" ; Protein_matches "WP:CE40797" ; CDS_matches "B0019.1" ; Times_observed "3"</span>
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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
36
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12763506 12763559 . - . Target "Mass_spec_peptide:MSP:FGHGQSLLAQGGMNEVVR" 1 18 ; Note "MSP:FGHGQSLLAQGGMNEVVR" ; Protein_matches "WP:CE40797" ; CDS_matches "B0019.1" ; Times_observed "1"</span>
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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
37
</td>
<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="plaintext">I SAGE_tag_unambiguously_mapped SAGE_tag 12763533 12763553 . - . Sequence SAGE:ggcagagtcttttggca;count 1;Gene amx-2;Transcript B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
38
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="plaintext">I mass_spec_genome translated_nucleotide_match 12764361 12764411 . - . Target "Mass_spec_peptide:MSP:NIQQNRPGLSVLVLEAR" 1 17 ; Note "MSP:NIQQNRPGLSVLVLEAR" ; Protein_matches "WP:CE40797" ; CDS_matches "B0019.1" ; Times_observed "2"</span>
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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
39
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="plaintext">I GenePair_STS PCR_product 12762449 12764118 . + . PCR_product "sjj_B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
40
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="plaintext">I Expr_profile experimental_result_region 12762449 12764118 . + . Expr_profile "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
41
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="plaintext">I Allele SNP 12764272 12764272 . + . Variation "snp_B0019[1]" ; Interpolated_map_position "14.003" ; ; RFLP "No"</span>
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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
42
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="plaintext">I Promoterome PCR_product 12764938 12766937 . + . PCR_product "p_B0019.1_93"</span>
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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
43
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="plaintext">I Oligo_set reagent 12759745 12761589 . - . Oligo_set "Aff_B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
44
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="plaintext">I Orfeome PCR_product 12759747 12764936 . - . PCR_product "mv_B0019.1" ; Amplified 1 ; Amplified 1</span>
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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
45
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="plaintext">I Coding_transcript three_prime_UTR 12759582 12759744 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
46
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="plaintext">I Coding_transcript coding_exon 12759745 12759828 . - 0 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
47
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="plaintext">I Coding_transcript coding_exon 12759949 12760013 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
48
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="plaintext">I Coding_transcript coding_exon 12760227 12760319 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
49
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="plaintext">I Coding_transcript coding_exon 12760365 12760494 . - 0 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
50
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="plaintext">I Coding_transcript coding_exon 12760834 12760904 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
51
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="plaintext">I Coding_transcript coding_exon 12761172 12761516 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
52
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="plaintext">I Coding_transcript coding_exon 12761799 12761953 . - 1 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
53
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="plaintext">I Coding_transcript coding_exon 12762127 12762268 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
54
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="plaintext">I Coding_transcript coding_exon 12762648 12762806 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
55
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="plaintext">I Coding_transcript coding_exon 12763112 12763249 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
56
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="plaintext">I Coding_transcript coding_exon 12763448 12763655 . - 0 Transcript "B0019.1" ; CDS "B0019.1"</span>
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57
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="plaintext">I Coding_transcript coding_exon 12763729 12763882 . - 1 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
58
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="plaintext">I Coding_transcript coding_exon 12763979 12764102 . - 2 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
59
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="plaintext">I Coding_transcript coding_exon 12764291 12764471 . - 0 Transcript "B0019.1" ; CDS "B0019.1"</span>
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60
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="plaintext">I Coding_transcript five_prime_UTR 12764938 12764949 . - . Transcript "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
61
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="plaintext">I Coding_transcript coding_exon 12764812 12764937 . - 0 Transcript "B0019.1" ; CDS "B0019.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="62" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
62
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="plaintext">X SAGE_tag SAGE_tag 6819353 6819366 . + . Sequence SAGE:aacggagccg;count 9;Gene amx-2;Transcript B0019.1</span>
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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
63
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="plaintext">X gene processed_transcript 944828 948883 . - . Gene "WBGene00004893"</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#90597a4495f86cc9aa824359f59cbfc74bba4474"><strong style="font-weight: bold;">Tests/GFF/wormbase_gff2_alt.txt</strong>
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1
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">Remanei_genome Genomic_canonical region 1 7816 . + . Sequence "Contig1020";</span>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="plaintext">Contig102 WU_MERGED CDS 1629 3377 . - . CDS "cr01.sctg102.wum.2.1"</span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">Contig102 WU_MERGED coding_exon 2927 3377 . - . CDS "cr01.sctg102.wum.2.1"</span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="plaintext">Contig102 WU_MERGED coding_exon 2474 2875 . - . CDS "cr01.sctg102.wum.2.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="plaintext">Contig102 WU_MERGED coding_exon 1928 2430 . - . CDS "cr01.sctg102.wum.2.1"</span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="plaintext">Contig102 WU_MERGED coding_exon 1629 1883 . - . CDS "cr01.sctg102.wum.2.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="plaintext">Contig102 WU_MERGED intron 2876 2926 . - . CDS "cr01.sctg102.wum.2.1"</span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="plaintext">Contig102 WU_MERGED intron 2431 2473 . - . CDS "cr01.sctg102.wum.2.1"</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">Contig102 WU_MERGED intron 1884 1927 . - . CDS "cr01.sctg102.wum.2.1"</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#936fbcee4a35275ed493abce9f6c9e7f4180931b"><strong style="font-weight: bold;">Tests/test_GFFSeqIOFeatureAdder.py</strong>
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""Test decoration of existing SeqRecords with GFF through a SeqIO interface.</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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3
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sys</span></span>
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4
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">os</span></span>
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5
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">unittest</span></span>
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6
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pprint</span></span>
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7
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC7" class="line" lang="python"></span>
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8
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">six</span></span>
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9
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>
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10
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
12
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
13
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
14
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>
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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
15
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio.SeqFeature</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqFeature</span><span class="p">,</span> <span class="n" style="color: #333;">FeatureLocation</span></span>
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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
16
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">BCBio.GFF</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">GFFExaminer</span><span class="p">,</span> <span class="n" style="color: #333;">GFFParser</span><span class="p">,</span> <span class="n" style="color: #333;">DiscoGFFParser</span><span class="p">)</span></span>
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17
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC18" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MapReduceGFFTest</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""Tests GFF parsing using a map-reduce framework for parallelization.</span></span>
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21
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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22
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC22" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">"GFF"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans_WS199_shortened_gff.txt"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_disco_host</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://localhost:7000"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC27" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_local_map_reduce</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"""General map reduce framework without parallelization.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
31
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">cds_limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span><span class="n" style="color: #333;">gff_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mRNA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">],</span> <span class="n" style="color: #333;">gff_id</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">])</span></span>
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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
32
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cds_limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
33
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">test_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
34
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">test_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">32</span></span>
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<td class="old_line diff-line-num old" data-linenumber="35" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
35
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC35" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
36
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_disco_map_reduce</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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37
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"""Map reduce framework parallelized using disco.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
39
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this needs to be more generalized but fails okay with no disco</span></span>
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<td class="old_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
40
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
41
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC41" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">disco</span></span>
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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
42
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC42" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">simplejson</span></span>
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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
43
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
44
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC44" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping -- disco and json not found"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
45
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="old_line diff-line-num old" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
46
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">cds_limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
47
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">'Non_coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
48
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC48" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">)],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
49
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">gff_id</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
50
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC50" class="line" lang="python"> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
51
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">DiscoGFFParser</span><span class="p">(</span><span class="n" style="color: #333;">disco_host</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_disco_host</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
52
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cds_limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
53
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">final_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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54
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># second gene feature is multi-parent</span></span>
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<td class="old_line diff-line-num old" data-linenumber="55" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="c1" style="color: #998; font-style: italic;"># two gene feature</span></span>
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56
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC56" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
57
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC57" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
58
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GFF3Test</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="59" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
59
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">"""Real live GFF3 tests from WormBase and NCBI.</span></span>
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60
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC60" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="61" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
61
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> Uses GFF3 data from:</span></span>
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62
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC62" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="63" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
63
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> ftp://ftp.wormbase.org/pub/wormbase/genomes/c_elegans/</span></span>
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<td class="old_line diff-line-num old" data-linenumber="64" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
64
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> genome_feature_tables/GFF3/</span></span>
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65
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC65" class="line" lang="python"><span class="s" style="color: #d14;"> ftp://ftp.wormbase.org/pub/wormbase/genomes/c_elegans/sequences/dna/</span></span>
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66
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC66" class="line" lang="python"></span>
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67
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> and from NCBI.</span></span>
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68
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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69
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC69" class="line" lang="python"></span>
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70
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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71
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">"GFF"</span><span class="p">)</span></span>
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72
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_seq_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans_WS199_dna_shortened.fa"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
73
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans_WS199_shortened_gff.txt"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
74
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_ann_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans_WS199_ann_gff.txt"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
75
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_full_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"/usr/home/chapmanb/mgh/ruvkun_rnai/wormbase/"</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<td class="old_line diff-line-num old" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
76
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">"data_files_WS198"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
77
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_ncbi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"ncbi_gff3.txt"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
78
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC78" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="79" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
79
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">not_t_full_celegans</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="80" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
80
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test the full C elegans chromosome and GFF files.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="81" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
81
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC81" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="82" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
82
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC82" class="line" lang="python"><span class="s" style="color: #d14;"> This is used to test GFF on large files and is not run as a standard</span></span>
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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
83
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> test. You will need to download the files and adjust the paths</span></span>
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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
84
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> to run this.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
85
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
86
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC86" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read the sequence information</span></span>
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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
87
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">seq_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_full_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans.WS199.dna.fa"</span><span class="p">)</span></span>
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88
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">gff_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_full_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans.WS199.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
89
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">seq_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="90" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
90
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">seq_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="91" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
91
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">seq_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
92
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC92" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#with open(gff_file) as gff_handle:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="93" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
93
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC93" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># possible_limits = feature_adder.available_limits(gff_handle)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="94" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
94
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC94" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pprint.pprint(possible_limits)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
95
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">rnai_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">'Orfeome'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'GenePair_STS'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Promoterome'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
96
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">gene_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">'Non_coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
97
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC97" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
98
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span><span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rnai_types</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gene_types</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="99" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
99
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">limit_info</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
100
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<td class="old_line diff-line-num old" data-linenumber="101" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
101
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC101" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
102
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_seq_dict</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="103" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
103
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">"""Internal reusable function to get the sequence dictionary.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="104" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
104
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
105
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">seq_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_seq_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="106" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
106
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">seq_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="107" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
107
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">seq_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
108
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq_dict</span></span>
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<td class="old_line diff-line-num old" data-linenumber="109" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
109
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC109" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
110
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_possible_limits</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
111
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC111" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate possible queries to limit a GFF file.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
112
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
113
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">gff_examiner</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFExaminer</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
114
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">possible_limits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff_examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">available_limits</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="115" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
115
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC115" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
116
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">pprint</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pprint</span><span class="p">(</span><span class="n" style="color: #333;">possible_limits</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
117
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC117" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
118
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_parent_child</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="119" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
119
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"""Summarize parent-child relationships in a GFF file.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="120" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
120
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
121
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">gff_examiner</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFExaminer</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
122
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">pc_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff_examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
123
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC123" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="124" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
124
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">pprint</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">pprint</span><span class="p">(</span><span class="n" style="color: #333;">pc_map</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
125
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC125" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
126
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_parent_child_file_modes</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="127" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
127
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">"""Summarize parent-child relationships in a GFF file.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
128
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="129" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
129
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">gff_examiner</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFExaminer</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
130
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC130" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use the loaded-from-filename as reference</span></span>
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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
131
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">pc_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff_examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
132
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC132" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="133" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
133
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"rt"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="134" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
134
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pc_map</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">gff_examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="135" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
135
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC135" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="136" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
136
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="137" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
137
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="n" style="color: #333;">PY2</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="138" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
138
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pc_map</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">gff_examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>
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139
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="140" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
140
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="141" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
141
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">gff_examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="142" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
142
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">TypeError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="143" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
143
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"input handle must be opened in text mode"</span><span class="p">,</span> <span class="n" style="color: #333;">e</span></span>
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<td class="old_line diff-line-num old" data-linenumber="144" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
144
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="145" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
145
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">"expected TypeError to be raised"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
146
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC146" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="147" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
147
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_flat_features</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="148" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
148
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check addition of flat non-nested features to multiple records.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="149" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
149
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="150" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
150
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_get_seq_dict</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
151
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">pcr_limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="152" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
152
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">'Orfeome'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'GenePair_STS'</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="153" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
153
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Promoterome'</span><span class="p">,</span> <span class="s" style="color: #d14;">'PCR_product'</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="154" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
154
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC154" class="line" lang="python"> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
155
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
156
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">pcr_limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
157
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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<td class="old_line diff-line-num old" data-linenumber="158" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
158
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'X'</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<td class="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
159
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC159" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="160" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
160
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_nested_features</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
161
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC161" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check three-deep nesting of features with gene, mRNA and CDS.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
162
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
163
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_get_seq_dict</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
164
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">cds_limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
165
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
166
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC166" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">)],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
167
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">gff_id</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
168
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC168" class="line" lang="python"> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
169
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
170
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cds_limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
171
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">final_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
172
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC172" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># first gene feature is plain</span></span>
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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
173
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="c1" style="color: #998; font-style: italic;"># two gene feature</span></span>
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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
174
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="c1" style="color: #998; font-style: italic;"># one transcript</span></span>
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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
175
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC175" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 15 final CDS regions</span></span>
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<td class="old_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
176
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">15</span></span>
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<td class="old_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
177
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC177" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="178" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
178
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_nested_multiparent_features</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
179
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"""Verify correct nesting of features with multiple parents.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
180
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
181
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_get_seq_dict</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="182" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
182
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">cds_limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="183" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
183
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
184
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC184" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">)],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="185" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
185
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">gff_id</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
186
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC186" class="line" lang="python"> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="187" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
187
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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188
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cds_limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="189" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
189
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">final_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="190" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
190
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC190" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># second gene feature is multi-parent</span></span>
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<td class="old_line diff-line-num old" data-linenumber="191" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
191
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="c1" style="color: #998; font-style: italic;"># two gene feature</span></span>
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<td class="old_line diff-line-num old" data-linenumber="192" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
192
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">cur_subs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span></span>
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<td class="old_line diff-line-num old" data-linenumber="193" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
193
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cur_subs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="c1" style="color: #998; font-style: italic;"># three transcripts</span></span>
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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
194
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC194" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the first and second transcript have the same CDSs</span></span>
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<td class="old_line diff-line-num old" data-linenumber="195" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
195
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cur_subs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>
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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
196
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">cur_subs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>
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<td class="old_line diff-line-num old" data-linenumber="197" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
197
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">cur_subs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">cur_subs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
198
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC198" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="199" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
199
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_no_dict_error</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="200" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
200
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC200" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure an error is raised when no dictionary to map to is present.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
201
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
202
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">(</span><span class="n" style="color: #333;">create_missing</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
203
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="204" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
204
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="205" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
205
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<td class="old_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
206
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC206" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># no error -- problem</span></span>
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<td class="old_line diff-line-num old" data-linenumber="207" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
207
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nc" style="color: #458; font-weight: 600;">AssertionError</span><span class="p">(</span><span class="s" style="color: #d14;">'Did not complain with missing dictionary'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="208" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
208
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="209" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
209
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<td class="old_line diff-line-num old" data-linenumber="210" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
210
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC210" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
211
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_unknown_seq</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="212" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
212
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC212" class="line" lang="python"> <span class="s" style="color: #d14;">"""Prepare unknown base sequences with the correct length.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="213" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
213
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="214" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
214
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
215
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"I"</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">12766937</span></span>
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<td class="old_line diff-line-num old" data-linenumber="216" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
216
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"X"</span><span class="p">].</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">17718531</span></span>
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<td class="old_line diff-line-num old" data-linenumber="217" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
217
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC217" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="218" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
218
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff_annotations</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="219" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
219
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC219" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check GFF annotations placed on an entire sequence.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="220" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
220
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="221" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
221
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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222
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_ann_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="223" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
223
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">final_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="224" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
224
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="old_line diff-line-num old" data-linenumber="225" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
225
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">'source'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'Expr_profile'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="226" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
226
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">final_rec</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">[</span><span class="s" style="color: #d14;">'expr_profile'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'B0019.1'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="227" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
227
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC227" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="228" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
228
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff3_iterator</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="229" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
229
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC229" class="line" lang="python"> <span class="s" style="color: #d14;">"""Iterated parsing in GFF3 files with nested features.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="230" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
230
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC230" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="231" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
231
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="232" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
232
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse_in_parts</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">target_lines</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">70</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="233" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
233
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC233" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># should be one big set because we don't have a good place to split</span></span>
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<td class="old_line diff-line-num old" data-linenumber="234" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
234
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>
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<td class="old_line diff-line-num old" data-linenumber="235" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
235
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">59</span></span>
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<td class="old_line diff-line-num old" data-linenumber="236" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
236
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC236" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="237" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
237
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff3_iterator_limit</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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238
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC238" class="line" lang="python"> <span class="s" style="color: #d14;">"""Iterated interface using a limit query on GFF3 files.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="239" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
239
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC239" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="240" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
240
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">cds_limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span></span>
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<td class="old_line diff-line-num old" data-linenumber="241" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
241
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="242" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
242
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC242" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'Coding_transcript'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">)],</span></span>
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<td class="old_line diff-line-num old" data-linenumber="243" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
243
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">gff_id</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="244" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
244
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC244" class="line" lang="python"> <span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="245" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
245
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="246" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
246
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cds_limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="247" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
247
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="248" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
248
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">tfeature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"I"</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="249" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
249
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sub_test</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="250" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
250
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">sub_test</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">,</span> <span class="n" style="color: #333;">sub_test</span></span>
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<td class="old_line diff-line-num old" data-linenumber="251" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
251
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC251" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="252" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
252
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff3_noval_attrib</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="253" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
253
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC253" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse GFF3 file from NCBI with a key/value pair with no value.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="254" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC254" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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255
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="256" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
256
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_ncbi</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="257" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
257
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="258" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
258
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">t_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="259" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
259
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">t_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"pseudo"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"true"</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="260" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
260
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC260" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="261" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
261
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff3_multiple_ids</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="262" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
262
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC262" class="line" lang="python"> <span class="s" style="color: #d14;">"""Deal with GFF3 with non-unique ID attributes, using NCBI example.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="263" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
263
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC263" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="264" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
264
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="265" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
265
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_ncbi</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="266" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
266
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="267" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
267
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">t_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="268" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
268
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC268" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 4 feature sets, same ID, different positions, different attributes</span></span>
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<td class="old_line diff-line-num old" data-linenumber="269" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
269
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">t_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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<td class="old_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
270
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">t_features</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
271
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>
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<td class="old_line diff-line-num old" data-linenumber="272" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
272
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC272" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="273" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
273
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_simple_parsing</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="274" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
274
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC274" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse GFF into a simple line by line dictionary without nesting.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="275" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
275
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="276" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
276
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
277
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="278" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
278
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse_simple</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
279
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="280" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
280
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">177</span><span class="p">,</span> <span class="n" style="color: #333;">num_lines</span></span>
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<td class="old_line diff-line-num old" data-linenumber="281" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
281
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">line_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'child'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="282" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
282
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'quals'</span><span class="p">][</span><span class="s" style="color: #d14;">'confirmed_est'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>
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<td class="old_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
283
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC283" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'yk1055g06.5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'OSTF085G5_1'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="284" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
284
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'location'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="mi" style="color: #099;">4582718</span><span class="p">,</span> <span class="mi" style="color: #099;">4583189</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="285" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
285
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC285" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="286" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
286
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_simple_parsing_nesting</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="287" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
287
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC287" class="line" lang="python"> <span class="s" style="color: #d14;">"""Simple parsing for lines with nesting, using the simplified API.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="288" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
288
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="289" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
289
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">test_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"transcripts.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="290" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
290
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="291" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
291
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse_simple</span><span class="p">(</span><span class="n" style="color: #333;">test_gff</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="292" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
292
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="293" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
293
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">16</span><span class="p">,</span> <span class="n" style="color: #333;">num_lines</span></span>
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<td class="old_line diff-line-num old" data-linenumber="294" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
294
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC294" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="295" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
295
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_extra_comma</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="296" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
296
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC296" class="line" lang="python"> <span class="s" style="color: #d14;">"""Correctly handle GFF3 files with extra trailing commas.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="297" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
297
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="298" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
298
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">tfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"mouse_extra_comma.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="299" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
299
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">in_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">tfile</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="300" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
300
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="301" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
301
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<td class="old_line diff-line-num old" data-linenumber="302" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
302
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="303" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
303
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">tested</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="old_line diff-line-num old" data-linenumber="304" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
304
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sub_top</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="305" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
305
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sub</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sub_top</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="306" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
306
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sub</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"Name"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"CDS:NC_000083.5:LOC100040603"</span><span class="p">]:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="307" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
307
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">tested</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="old_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
308
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"Parent"</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="309" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
309
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tested</span><span class="p">,</span> <span class="s" style="color: #d14;">"Did not find sub-feature to test"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
310
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC310" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="311" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
311
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_novalue_key</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="312" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
312
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC312" class="line" lang="python"> <span class="s" style="color: #d14;">"""Handle GFF3 files with keys and no values.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="313" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
313
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="314" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
314
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">tfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"glimmer_nokeyval.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="315" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
315
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">next</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">tfile</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="316" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
316
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span></span>
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<td class="old_line diff-line-num old" data-linenumber="317" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
317
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'ID'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'GL0000006'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="318" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
318
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="old_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
319
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"Lack 3'-end"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"true"</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="320" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
320
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="s" style="color: #d14;">"ID"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">qualifiers</span></span>
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<td class="old_line diff-line-num old" data-linenumber="321" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
321
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"Complete"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"true"</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="322" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
322
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC322" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="323" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
323
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_key_whitespace</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
324
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC324" class="line" lang="python"> <span class="s" style="color: #d14;">"""Fix keys with problematic whitespace.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="325" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
325
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC325" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="326" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
326
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">tfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"spaces.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="327" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
327
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">line_info</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse_simple</span><span class="p">(</span><span class="n" style="color: #333;">tfile</span><span class="p">)):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="328" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
328
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="329" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
329
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">][</span><span class="s" style="color: #d14;">"foo"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">"bar"</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="330" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
330
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC330" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="331" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
331
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_trans_spliicing</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="332" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
332
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC332" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parsing of transspliced genes from GFF3 spec where child locations don't match to parents.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="333" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
333
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC333" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="334" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
334
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"trans_splicing.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="335" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
335
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">in_handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
336
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">six</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">next</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">))</span></span>
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337
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="old_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
338
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"gene83"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="339" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
339
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="old_line diff-line-num old" data-linenumber="340" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
340
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span></span>
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<td class="old_line diff-line-num old" data-linenumber="341" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
341
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC341" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="342" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
342
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"gene84"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="343" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
343
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="old_line diff-line-num old" data-linenumber="344" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
344
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span></span>
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<td class="old_line diff-line-num old" data-linenumber="345" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
345
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC345" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="346" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
346
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC346" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="347" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
347
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC347" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SolidGFFTester</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="348" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
348
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC348" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test reading output from SOLiD analysis, as GFF3.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="349" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
349
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC349" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
350
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;"> See more details on SOLiD GFF here:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="351" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
351
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC351" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="352" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
352
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;"> http://solidsoftwaretools.com/gf/project/matogff/</span></span>
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<td class="old_line diff-line-num old" data-linenumber="353" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
353
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC353" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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354
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC354" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="355" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
355
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="356" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
356
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">"GFF"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="357" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
357
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"F3-unique-3.v2.gff"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="358" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
358
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC358" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="359" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
359
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_basic_solid_parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="360" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
360
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC360" class="line" lang="python"> <span class="s" style="color: #d14;">"""Basic parsing of SOLiD GFF results files.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="361" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
361
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC361" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="362" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
362
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="363" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
363
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="364" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
364
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">test_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'3_341_424_F3'</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="365" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
365
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC365" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">location</span><span class="p">.</span><span class="n" style="color: #333;">nofuzzy_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">102716</span></span>
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<td class="old_line diff-line-num old" data-linenumber="366" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
366
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">location</span><span class="p">.</span><span class="n" style="color: #333;">nofuzzy_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">102736</span></span>
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<td class="old_line diff-line-num old" data-linenumber="367" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
367
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span></span>
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<td class="old_line diff-line-num old" data-linenumber="368" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
368
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'score'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'10.6'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="369" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
369
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC369" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'source'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'solid'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="370" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
370
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC370" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="371" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
371
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'read'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="372" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
372
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'g'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'T2203031313223113212'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="373" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
373
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'q'</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">20</span></span>
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<td class="old_line diff-line-num old" data-linenumber="374" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
374
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC374" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="375" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
375
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_solid_iterator</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="376" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
376
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC376" class="line" lang="python"> <span class="s" style="color: #d14;">"""Iterated parsing in a flat file without nested features.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="377" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
377
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="378" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
378
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="379" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
379
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">feature_sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="380" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
380
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC380" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse_in_parts</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">,</span> <span class="n" style="color: #333;">target_lines</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="381" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
381
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">feature_sizes</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="382" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
382
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">feature_sizes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">112</span></span>
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<td class="old_line diff-line-num old" data-linenumber="383" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
383
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">max</span><span class="p">(</span><span class="n" style="color: #333;">feature_sizes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="384" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
384
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC384" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="385" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
385
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_line_adjust</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="386" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
386
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC386" class="line" lang="python"> <span class="s" style="color: #d14;">"""Adjust lines during parsing to fix potential GFF problems.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="387" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
387
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC387" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="388" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
388
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC388" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="389" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
389
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">adjust_fn</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="390" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
390
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">rec_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="s" style="color: #d14;">'quals'</span><span class="p">][</span><span class="s" style="color: #d14;">'i'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="391" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
391
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="392" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
392
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="s" style="color: #d14;">'quals'</span><span class="p">][</span><span class="s" style="color: #d14;">'read_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">read_name</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="393" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
393
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_index</span></span>
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<td class="old_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
394
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC394" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">results</span></span>
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<td class="old_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
395
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC395" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
396
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">(</span><span class="n" style="color: #333;">line_adjust_fn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">adjust_fn</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="397" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
397
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="398" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
398
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="399" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
399
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">work_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="400" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
400
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">work_rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'1'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="401" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
401
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">work_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">112</span></span>
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<td class="old_line diff-line-num old" data-linenumber="402" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
402
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">work_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'read_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>
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<td class="old_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
403
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC403" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'3_336_815_F3'</span><span class="p">]</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC404" class="line" lang="python"></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC405" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="406" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
406
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC406" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GFF2Tester</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="407" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
407
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC407" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse GFF2 and GTF files, building features.</span></span>
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408
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC408" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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409
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC409" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="410" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
410
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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411
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">"GFF"</span><span class="p">)</span></span>
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412
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ensembl_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"ensembl_gtf.txt"</span><span class="p">)</span></span>
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413
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"wormbase_gff2.txt"</span><span class="p">)</span></span>
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414
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_jgi_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"jgi_gff2.txt"</span><span class="p">)</span></span>
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415
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wb_alt_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"wormbase_gff2_alt.txt"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="416" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
416
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC416" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="417" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
417
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_basic_attributes</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="418" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
418
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC418" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse out basic attributes of GFF2 from Ensembl GTF.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
419
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC419" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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420
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span><span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">'snoRNA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'exon'</span><span class="p">)])</span></span>
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<td class="old_line diff-line-num old" data-linenumber="421" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
421
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ensembl_file</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="422" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
422
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">work_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="423" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
423
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">work_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="424" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
424
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">test_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">work_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="425" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
425
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">qual_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">())</span></span>
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<td class="old_line diff-line-num old" data-linenumber="426" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
426
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">qual_keys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">sort</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="427" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
427
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">qual_keys</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span></span>
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<td class="old_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
428
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC428" class="line" lang="python"> <span class="s" style="color: #d14;">'Parent'</span><span class="p">,</span> <span class="s" style="color: #d14;">'exon_number'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene_id'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'source'</span><span class="p">,</span> <span class="s" style="color: #d14;">'transcript_id'</span><span class="p">,</span> <span class="s" style="color: #d14;">'transcript_name'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="429" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
429
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC429" class="line" lang="python"> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="430" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
430
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'source'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'snoRNA'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="431" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
431
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'transcript_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'NR_001477.2'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="432" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
432
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC432" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'exon_number'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="433" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
433
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC433" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="434" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
434
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC434" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_tricky_semicolons</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="435" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
435
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC435" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parsing of tricky semi-colon positions in WormBase GFF2.</span></span>
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436
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC436" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="437" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
437
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">dict</span><span class="p">(</span><span class="n" style="color: #333;">gff_source_type</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">'Genomic_canonical'</span><span class="p">,</span> <span class="s" style="color: #d14;">'region'</span><span class="p">)])</span></span>
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<td class="old_line diff-line-num old" data-linenumber="438" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
438
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">limit_info</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="439" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
439
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">work_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'I'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="440" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
440
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">work_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="441" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
441
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">test_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">work_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="442" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
442
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'Note'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>
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<td class="old_line diff-line-num old" data-linenumber="443" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
443
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC443" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">'Clone cTel33B; Genbank AC199162'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Clone cTel33B; Genbank AC199162'</span><span class="p">],</span> <span class="n" style="color: #333;">test_feature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"Note"</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="444" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
444
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC444" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="445" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
445
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_unescaped_semicolons</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="446" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
446
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC446" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse inputs with unescaped semi-colons.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="447" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
447
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC447" class="line" lang="python"><span class="s" style="color: #d14;"> This is a band-aid to not fail rather than correct parsing, since</span></span>
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<td class="old_line diff-line-num old" data-linenumber="448" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
448
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC448" class="line" lang="python"><span class="s" style="color: #d14;"> the combined feature will not be maintained.</span></span>
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449
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC449" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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450
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"unescaped-semicolon.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="451" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
451
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>
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452
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'chr1'</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="453" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
453
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC453" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"Description"</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'osFTL6'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="454" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
454
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"Description"</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'protein, expressed'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="455" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
455
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC455" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="456" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
456
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_jgi_gff</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="457" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
457
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC457" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parsing of JGI formatted GFF2, nested using transcriptId and proteinID</span></span>
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<td class="old_line diff-line-num old" data-linenumber="458" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
458
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC458" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="459" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
459
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_jgi_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="460" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
460
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">tfeature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'chr_1'</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="461" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
461
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC461" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">location</span><span class="p">.</span><span class="n" style="color: #333;">nofuzzy_start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">37060</span></span>
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<td class="old_line diff-line-num old" data-linenumber="462" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
462
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC462" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">location</span><span class="p">.</span><span class="n" style="color: #333;">nofuzzy_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">38216</span></span>
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<td class="old_line diff-line-num old" data-linenumber="463" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
463
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC463" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'inferred_parent'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="464" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
464
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>
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<td class="old_line diff-line-num old" data-linenumber="465" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
465
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">sfeature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="466" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
466
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">sfeature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'proteinId'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'873'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="467" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
467
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">sfeature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">'phase'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'0'</span><span class="p">]</span></span>
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468
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC468" class="line" lang="python"></span>
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469
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC469" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_ensembl_nested_features</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="470" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
470
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC470" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test nesting of features with GFF2 files using transcript_id.</span></span>
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471
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC471" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="472" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
472
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC472" class="line" lang="python"><span class="s" style="color: #d14;"> XXX sub_features no longer supported in Biopython</span></span>
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<td class="old_line diff-line-num old" data-linenumber="473" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
473
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC473" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="474" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
474
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ensembl_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="475" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
475
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"I"</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="old_line diff-line-num old" data-linenumber="476" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
476
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">t_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"I"</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="477" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
477
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC477" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#assert len(t_feature.sub_features) == 32, len(t_feature.sub_features)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="478" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
478
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC478" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="479" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
479
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_wormbase_nested_features</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="480" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
480
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC480" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test nesting of features with GFF2 files using Transcript only.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="481" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
481
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC481" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="482" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
482
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="483" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
483
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>
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<td class="old_line diff-line-num old" data-linenumber="484" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
484
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC484" class="line" lang="python"> <span class="n" style="color: #333;">parent_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">f</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"I"</span><span class="p">].</span><span class="n" style="color: #333;">features</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Transcript"</span><span class="p">]</span></span>
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485
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC485" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">parent_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="486" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
486
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">inferred_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">f</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"I"</span><span class="p">].</span><span class="n" style="color: #333;">features</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"inferred_parent"</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="487" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
487
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">inferred_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="488" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
488
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">tfeature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent_features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="489" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
489
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">qualifiers</span><span class="p">[</span><span class="s" style="color: #d14;">"WormPep"</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"WP:CE40797"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="490" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
490
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">46</span></span>
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<td class="old_line diff-line-num old" data-linenumber="491" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
491
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC491" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="492" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
492
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC492" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_wb_cds_nested_features</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="493" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
493
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC493" class="line" lang="python"> <span class="s" style="color: #d14;">"""Nesting of GFF2 features with a flat CDS key value pair.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="494" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
494
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC494" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="495" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
495
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">rec_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wb_alt_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="496" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
496
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC496" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="old_line diff-line-num old" data-linenumber="497" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
497
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">features</span></span>
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<td class="old_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
498
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="499" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
499
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">tfeature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="500" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
500
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC500" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"cr01.sctg102.wum.2.1"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="501" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
501
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC501" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">tfeature</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">7</span></span>
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<td class="old_line diff-line-num old" data-linenumber="502" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
502
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC502" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="503" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
503
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC503" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff2_iteration</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="504" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
504
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC504" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test iterated features with GFF2 files, breaking without parents.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="505" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
505
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC505" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="506" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
506
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="507" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
507
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC507" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span><span class="p">,</span> <span class="n" style="color: #333;">target_lines</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">15</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="508" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
508
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="509" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
509
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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<td class="old_line diff-line-num old" data-linenumber="510" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
510
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'region'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
511
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'SAGE_tag'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="512" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
512
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC512" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">sub_features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">29</span></span>
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<td class="old_line diff-line-num old" data-linenumber="513" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
513
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC513" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="514" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
514
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC514" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="515" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
515
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC515" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DirectivesTest</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="516" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
516
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC516" class="line" lang="python"> <span class="s" style="color: #d14;">"""Tests for parsing directives and other meta-data.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="517" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
517
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC517" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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518
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC518" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="519" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
519
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC519" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="520" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
520
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">"GFF"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="521" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
521
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"hybrid1.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="522" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
522
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ncbi_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"hybrid2.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="523" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
523
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ncbi_fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"hybrid2.fa"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="524" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
524
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_problem_seq_region_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"problem_sequence_region.gff3"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="525" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
525
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC525" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="526" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
526
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC526" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_basic_directives</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="527" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
527
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC527" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse out top level meta-data supplied in a GFF3 file.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="528" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
528
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC528" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="529" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
529
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="530" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
530
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC530" class="line" lang="python"> <span class="n" style="color: #333;">anns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'chr17'</span><span class="p">].</span><span class="n" style="color: #333;">annotations</span></span>
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<td class="old_line diff-line-num old" data-linenumber="531" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
531
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC531" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">anns</span><span class="p">[</span><span class="s" style="color: #d14;">'gff-version'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'3'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="532" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
532
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">anns</span><span class="p">[</span><span class="s" style="color: #d14;">'attribute-ontology'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'baz'</span><span class="p">]</span></span>
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533
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC533" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">anns</span><span class="p">[</span><span class="s" style="color: #d14;">'feature-ontology'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'bar'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="534" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
534
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC534" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">anns</span><span class="p">[</span><span class="s" style="color: #d14;">'source-ontology'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'boo'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="535" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
535
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">anns</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence-region'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'chr17'</span><span class="p">,</span> <span class="mi" style="color: #099;">62467933</span><span class="p">,</span> <span class="mi" style="color: #099;">62469545</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="536" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
536
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC536" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="537" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
537
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC537" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_fasta_directive</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="538" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
538
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC538" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse FASTA sequence information contained in a GFF3 file.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="539" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
539
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC539" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="540" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
540
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="541" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
541
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="542" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
542
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">test_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'chr17'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="543" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
543
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">test_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"GATTACAGATTACA"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="544" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
544
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC544" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="545" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
545
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_fasta_directive_w_ncbi</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="546" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
546
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC546" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse FASTA sequence information contained in a GFF3 file with NCBI style IDs.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="547" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
547
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC547" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="548" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
548
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC548" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nf" style="color: #900; font-weight: 600;">open</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ncbi_fa</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">seq_handle</span><span class="p">:</span></span>
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549
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">seq_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="550" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
550
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ncbi_gff</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="551" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
551
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="552" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
552
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">test_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'lcl|chr17'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="553" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
553
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">test_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"GATTACAGATTACA"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="554" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
554
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC554" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="555" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
555
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_fasta_directive_w_ncbi_fa</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="556" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
556
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC556" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse FASTA sequence information contained in a separate file with NCBI style IDs.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="557" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
557
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC557" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="558" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
558
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ncbi_gff</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="559" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
559
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="560" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
560
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">test_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'chr17'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="561" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
561
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC561" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">test_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"GATTACAGATTACA"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="562" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
562
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC562" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="563" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
563
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_examiner_with_fasta</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="564" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
564
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC564" class="line" lang="python"> <span class="s" style="color: #d14;">"""Perform high level examination of files with FASTA directives.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="565" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
565
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC565" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="566" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
566
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC566" class="line" lang="python"> <span class="n" style="color: #333;">examiner</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">GFFExaminer</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="567" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
567
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">pc_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="568" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
568
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC568" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pc_map</span><span class="p">[(</span><span class="s" style="color: #d14;">'UCSC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[(</span><span class="s" style="color: #d14;">'UCSC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="569" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
569
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">limits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">examiner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">available_limits</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="570" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
570
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">limits</span><span class="p">[</span><span class="s" style="color: #d14;">'gff_id'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'chr17'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="571" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
571
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC571" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">limits</span><span class="p">[</span><span class="s" style="color: #d14;">'gff_source_type'</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> \</span>
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<td class="old_line diff-line-num old" data-linenumber="572" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
572
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC572" class="line" lang="python"> <span class="p">[(</span><span class="s" style="color: #d14;">'UCSC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CDS'</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'UCSC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mRNA'</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="573" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
573
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC573" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="574" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
574
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC574" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_problem_sequence_region</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="575" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
575
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC575" class="line" lang="python"> <span class="s" style="color: #d14;">"""Avoid issues with sequence region directives lacking contigs</span></span>
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<td class="old_line diff-line-num old" data-linenumber="576" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
576
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC576" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="577" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
577
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_problem_seq_region_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="578" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
578
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC578" class="line" lang="python"> <span class="n" style="color: #333;">anns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">].</span><span class="n" style="color: #333;">annotations</span></span>
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<td class="old_line diff-line-num old" data-linenumber="579" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
579
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC579" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">anns</span><span class="p">[</span><span class="s" style="color: #d14;">'gff-version'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'3'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="580" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
580
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC580" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">anns</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence-region'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2482535</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="581" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
581
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC581" class="line" lang="python"></span>
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582
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC582" class="line" lang="python"></span>
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583
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC583" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">OutputTest</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="584" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
584
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC584" class="line" lang="python"> <span class="s" style="color: #d14;">"""Tests to write SeqFeatures to GFF3 output format.</span></span>
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585
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC585" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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586
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC586" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="587" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
587
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC587" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setUp</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="588" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
588
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC588" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">),</span> <span class="s" style="color: #d14;">"GFF"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="589" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
589
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_seq_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans_WS199_dna_shortened.fa"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="590" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
590
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC590" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans_WS199_shortened_gff.txt"</span><span class="p">)</span></span>
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591
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_ann_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"c_elegans_WS199_ann_gff.txt"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="592" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
592
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">join</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"wormbase_gff2.txt"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="593" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
593
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC593" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="594" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
594
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC594" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff3_to_gff3</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="595" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
595
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC595" class="line" lang="python"> <span class="s" style="color: #d14;">"""Read in and write out GFF3 without any loss of information.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="596" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
596
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC596" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="597" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
597
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">))</span></span>
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598
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">StringIO</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="599" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
599
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="600" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
600
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC600" class="line" lang="python"> <span class="n" style="color: #333;">wrote_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getvalue</span><span class="p">())</span></span>
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<td class="old_line diff-line-num old" data-linenumber="601" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
601
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">recs_two</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">wrote_handle</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="602" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
602
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC602" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="603" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
603
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC603" class="line" lang="python"> <span class="n" style="color: #333;">orig_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="604" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
604
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">re_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="605" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
605
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC605" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">orig_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nf" style="color: #900; font-weight: 600;">len</span><span class="p">(</span><span class="n" style="color: #333;">re_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="606" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
606
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC606" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">orig_f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nf" style="color: #900; font-weight: 600;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">orig_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="607" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
607
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC607" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">orig_f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">re_rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<td class="old_line diff-line-num old" data-linenumber="608" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
608
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC608" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="609" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
609
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC609" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_gff2_to_gff3</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="610" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
610
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC610" class="line" lang="python"> <span class="s" style="color: #d14;">"""Read in GFF2 and write out as GFF3.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="611" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
611
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC611" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="612" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
612
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="613" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
613
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">StringIO</span><span class="p">()</span></span>
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614
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="615" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
615
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC615" class="line" lang="python"> <span class="n" style="color: #333;">wrote_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getvalue</span><span class="p">())</span></span>
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<td class="old_line diff-line-num old" data-linenumber="616" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
616
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC616" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check some tricky lines in the GFF2 file</span></span>
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<td class="old_line diff-line-num old" data-linenumber="617" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
617
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC617" class="line" lang="python"> <span class="n" style="color: #333;">checks</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="618" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
618
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">wrote_handle</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="619" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
619
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"Interpolated_map_position"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="620" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
620
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC620" class="line" lang="python"> <span class="n" style="color: #333;">checks</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="621" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
621
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC621" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"RFLP=No"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="622" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
622
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC622" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"Gene=WBGene00000138"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="623" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
623
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">checks</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="624" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
624
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"ID=B0019.1"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="625" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
625
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC625" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"translated_nucleotide_match</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">12762127"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="626" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
626
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC626" class="line" lang="python"> <span class="n" style="color: #333;">checks</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="old_line diff-line-num old" data-linenumber="627" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
627
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"Note=MSP:FADFSPLDVSDVNFATDDLAK"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="628" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
628
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">checks</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">"Missing check line"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="629" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
629
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC629" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="630" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
630
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC630" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_write_from_recs</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="631" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
631
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC631" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write out GFF3 from SeqRecord inputs.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="632" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
632
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC632" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="633" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
633
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC633" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Seq</span><span class="p">(</span><span class="s" style="color: #d14;">"GATCGATCGATCGATCGATC"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="634" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
634
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="s" style="color: #d14;">"ID1"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="635" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
635
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">qualifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"source"</span><span class="p">:</span> <span class="s" style="color: #d14;">"prediction"</span><span class="p">,</span> <span class="s" style="color: #d14;">"score"</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">"other"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"Some"</span><span class="p">,</span> <span class="s" style="color: #d14;">"annotations"</span><span class="p">],</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">:</span> <span class="s" style="color: #d14;">"gene1"</span><span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="636" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
636
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC636" class="line" lang="python"> <span class="n" style="color: #333;">sub_qualifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"source"</span><span class="p">:</span> <span class="s" style="color: #d14;">"prediction"</span><span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
637
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC637" class="line" lang="python"> <span class="n" style="color: #333;">top_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SeqFeature</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">FeatureLocation</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene"</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qualifiers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualifiers</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="638" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
638
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC638" class="line" lang="python"> <span class="n" style="color: #333;">top_feature</span><span class="p">.</span><span class="n" style="color: #333;">sub_features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<td class="old_line diff-line-num old" data-linenumber="639" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
639
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC639" class="line" lang="python"> <span class="nc" style="color: #458; font-weight: 600;">SeqFeature</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">FeatureLocation</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"exon"</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qualifiers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sub_qualifiers</span><span class="p">),</span></span>
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<td class="old_line diff-line-num old" data-linenumber="640" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
640
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC640" class="line" lang="python"> <span class="nc" style="color: #458; font-weight: 600;">SeqFeature</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">FeatureLocation</span><span class="p">(</span><span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"exon"</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qualifiers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sub_qualifiers</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="641" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
641
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC641" class="line" lang="python"> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="642" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
642
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC642" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">top_feature</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="643" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
643
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC643" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">StringIO</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
644
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">([</span><span class="n" style="color: #333;">rec</span><span class="p">],</span> <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>
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645
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">wrote_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getvalue</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="646" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
646
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC646" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">wrote_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"##gff-version 3"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
647
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC647" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">wrote_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"##sequence-region ID1 1 20"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="648" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
648
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC648" class="line" lang="python"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">wrote_info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">))</span></span>
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<td class="old_line diff-line-num old" data-linenumber="649" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
649
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC649" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">wrote_info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span></span>
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<td class="old_line diff-line-num old" data-linenumber="650" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
650
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC650" class="line" lang="python"> <span class="s" style="color: #d14;">'ID1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'prediction'</span><span class="p">,</span> <span class="s" style="color: #d14;">'gene'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'20'</span><span class="p">,</span> <span class="s" style="color: #d14;">'10.0'</span><span class="p">,</span> <span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ID=gene1;other=Some,annotations'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="651" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
651
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC651" class="line" lang="python"> <span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="652" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
652
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC652" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">wrote_info</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'ID1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'prediction'</span><span class="p">,</span> <span class="s" style="color: #d14;">'exon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Parent=gene1'</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="653" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
653
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC653" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="654" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
654
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC654" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_write_fasta</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="655" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
655
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC655" class="line" lang="python"> <span class="s" style="color: #d14;">"""Include FASTA records in GFF output.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="656" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
656
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC656" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="657" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
657
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC657" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Seq</span><span class="p">(</span><span class="s" style="color: #d14;">"GATCGATCGATCGATCGATC"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="658" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
658
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC658" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="s" style="color: #d14;">"ID1"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
659
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC659" class="line" lang="python"> <span class="n" style="color: #333;">qualifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"source"</span><span class="p">:</span> <span class="s" style="color: #d14;">"prediction"</span><span class="p">,</span> <span class="s" style="color: #d14;">"score"</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">"other"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"Some"</span><span class="p">,</span> <span class="s" style="color: #d14;">"annotations"</span><span class="p">],</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">:</span> <span class="s" style="color: #d14;">"gene1"</span><span class="p">}</span></span>
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660
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC660" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nc" style="color: #458; font-weight: 600;">SeqFeature</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">FeatureLocation</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene"</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qualifiers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualifiers</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="661" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
661
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC661" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">StringIO</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="662" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
662
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC662" class="line" lang="python"> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">([</span><span class="n" style="color: #333;">rec</span><span class="p">],</span> <span class="n" style="color: #333;">out_handle</span><span class="p">,</span> <span class="n" style="color: #333;">include_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="663" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
663
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">wrote_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getvalue</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="664" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
664
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC664" class="line" lang="python"> <span class="n" style="color: #333;">fasta_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wrote_info</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">:]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="665" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
665
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC665" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"##FASTA"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="666" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
666
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta_parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">">ID1 <unknown description>"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="667" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
667
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC667" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">fasta_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nf" style="color: #900; font-weight: 600;">str</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="668" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
668
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC668" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="669" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
669
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC669" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_write_seqrecord</span><span class="p">(</span><span class="n" style="color: #333;">self</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="670" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
670
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC670" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write single SeqRecords.</span></span>
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<td class="old_line diff-line-num old" data-linenumber="671" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
671
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC671" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="old_line diff-line-num old" data-linenumber="672" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
672
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC672" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Seq</span><span class="p">(</span><span class="s" style="color: #d14;">"GATCGATCGATCGATCGATC"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="673" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
673
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC673" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SeqRecord</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="s" style="color: #d14;">"ID1"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="674" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
674
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">qualifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"source"</span><span class="p">:</span> <span class="s" style="color: #d14;">"prediction"</span><span class="p">,</span> <span class="s" style="color: #d14;">"score"</span><span class="p">:</span> <span class="mf" style="color: #099;">10.0</span><span class="p">,</span> <span class="s" style="color: #d14;">"other"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"Some"</span><span class="p">,</span> <span class="s" style="color: #d14;">"annotations"</span><span class="p">],</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">:</span> <span class="s" style="color: #d14;">"gene1"</span><span class="p">}</span></span>
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675
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">features</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nc" style="color: #458; font-weight: 600;">SeqFeature</span><span class="p">(</span><span class="nc" style="color: #458; font-weight: 600;">FeatureLocation</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene"</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">qualifiers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualifiers</span><span class="p">)]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
676
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">StringIO</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="677" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
677
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">([</span><span class="n" style="color: #333;">rec</span><span class="p">],</span> <span class="n" style="color: #333;">out_handle</span><span class="p">,</span> <span class="n" style="color: #333;">include_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="678" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
678
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">wrote_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">getvalue</span><span class="p">().</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="679" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
679
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">gff_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wrote_info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="680" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
680
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC680" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">gff_line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ID1"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="681" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
681
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC681" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
682
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC682" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="683" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
683
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC683" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_tests</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">):</span></span>
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<td class="old_line diff-line-num old" data-linenumber="684" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
684
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC684" class="line" lang="python"> <span class="n" style="color: #333;">test_suite</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">testing_suite</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="685" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
685
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">TextTestRunner</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">verbosity</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="686" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
686
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC686" class="line" lang="python"> <span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333;">test_suite</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="687" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
687
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC687" class="line" lang="python"></span>
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688
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC688" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="689" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
689
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC689" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">testing_suite</span><span class="p">():</span></span>
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<td class="old_line diff-line-num old" data-linenumber="690" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
690
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC690" class="line" lang="python"> <span class="s" style="color: #d14;">"""Generate the suite of tests.</span></span>
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691
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC691" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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692
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">test_suite</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">TestSuite</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="693" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
693
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;">test_loader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unittest</span><span class="p">.</span><span class="nc" style="color: #458; font-weight: 600;">TestLoader</span><span class="p">()</span></span>
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<td class="old_line diff-line-num old" data-linenumber="694" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
694
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC694" class="line" lang="python"> <span class="n" style="color: #333;">test_loader</span><span class="p">.</span><span class="n" style="color: #333;">testMethodPrefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'t_'</span></span>
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<td class="old_line diff-line-num old" data-linenumber="695" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
695
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC695" class="line" lang="python"> <span class="n" style="color: #333;">tests</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">GFF3Test</span><span class="p">,</span> <span class="n" style="color: #333;">MapReduceGFFTest</span><span class="p">,</span> <span class="n" style="color: #333;">SolidGFFTester</span><span class="p">,</span> <span class="n" style="color: #333;">GFF2Tester</span><span class="p">,</span> <span class="n" style="color: #333;">DirectivesTest</span><span class="p">,</span> <span class="n" style="color: #333;">OutputTest</span><span class="p">]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="696" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
696
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC696" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#tests = [GFF3Test]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="697" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
697
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC697" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">test</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tests</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
698
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC698" class="line" lang="python"> <span class="n" style="color: #333;">cur_suite</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">test_loader</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">loadTestsFromTestCase</span><span class="p">(</span><span class="n" style="color: #333;">test</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="699" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
699
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC699" class="line" lang="python"> <span class="n" style="color: #333;">test_suite</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">addTest</span><span class="p">(</span><span class="n" style="color: #333;">cur_suite</span><span class="p">)</span></span>
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700
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC700" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_suite</span></span>
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<td class="old_line diff-line-num old" data-linenumber="701" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
701
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC701" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="702" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
702
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC702" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="703" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
703
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC703" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="704" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
704
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<td class="new_line diff-line-num old" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC704" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">exit</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">run_tests</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">))</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#788d776bfe907f02f738f7115e219184170cb4f7"><strong style="font-weight: bold;">bcbio_gff.egg-info/PKG-INFO</strong></a>
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1
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC1" class="line" lang="plaintext">Metadata-Version: <span class="idiff left right deletion" style="background-color: #fac5cd;">1.0</span></span>
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1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">Metadata-Version: <span class="idiff left right addition" style="background-color: #c7f0d2;">2.1</span></span>
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2
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2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext">Name: bcbio-gff</span>
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3
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<td class="new_line diff-line-num old" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right deletion" style="background-color: #fac5cd;">6.9</span></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right addition" style="background-color: #c7f0d2;">7.0</span></span>
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="plaintext">Summary: Read and write Generic Feature Format (GFF) with Biopython integration.</span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/chapmanb/bcbb/tree/master/gff</span>
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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC6" class="line" lang="plaintext">Author: Brad Chapman</span>
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="plaintext">Author-email: chapmanb@50mail.com</span>
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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="plaintext">License: Biopython License</span>
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<td class="old_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC9" class="line" lang="plaintext">Description: UNKNOWN</span>
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC10" class="line" lang="plaintext">Platform: UNKNOWN</span></pre></td>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext">License-File: LICENSE</span></pre></td>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/112984ef376a389973c42d6ece673e459503c410#944df03d39008ed8c63cac4c573db3e9218908ca"><strong style="font-weight: bold;">bcbio_gff.egg-info/SOURCES.txt</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -8,31 +8,6 @@ BCBio/GFF/GFFOutput.py</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="plaintext">BCBio/GFF/GFFParser.py</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext">BCBio/GFF/__init__.py</span>
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC10" class="line" lang="plaintext">BCBio/GFF/_utils.py</span>
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<td class="old_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
11
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC11" class="line" lang="plaintext">Scripts/gff/access_gff_index.py</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC12" class="line" lang="plaintext">Scripts/gff/genbank_to_gff.py</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC13" class="line" lang="plaintext">Scripts/gff/gff2_to_gff3.py</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC14" class="line" lang="plaintext">Scripts/gff/gff_to_biosql.py</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC15" class="line" lang="plaintext">Scripts/gff/gff_to_genbank.py</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC16" class="line" lang="plaintext">Tests/test_GFFSeqIOFeatureAdder.py</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC17" class="line" lang="plaintext">Tests/GFF/F3-unique-3.v2.gff</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC11" class="line" lang="plaintext">bcbio_gff.egg-info/PKG-INFO</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC12" class="line" lang="plaintext">bcbio_gff.egg-info/SOURCES.txt</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 0.875rem; color: #333238; position: relative; font-family: var(--default-mono-font, "Menlo"),"DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC13" class="line" lang="plaintext">bcbio_gff.egg-info/dependency_links.txt</span>
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