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GitLab

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<h3>

Étienne Mollier pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/python-bcbio-gff">Debian Med / python-bcbio-gff</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6">0195e227</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2021-10-09T21:21:38+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.7</pre>

</li>

</ul>

<h4>30 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#ba3404825a4d349f45211497986428bd4b75a757">

BCBio/GFF/GFFParser.py

</a>

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<li class="file-stats">

<a href="#377317303b32a87f51356a964b30d05b7cf78ba3">

BCBio/GFF/__init__.py

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<li class="file-stats">

<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

PKG-INFO

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<li class="file-stats">

<a href="#05ff4d05b4718a5c1e7de6afef599c230c721357">

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+

Scripts/gff/access_gff_index.py

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<a href="#41731cf6f4dd9bb65e654cdbac1505e47ccb8f13">

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Scripts/gff/genbank_to_gff.py

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Scripts/gff/gff2_to_gff3.py

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Scripts/gff/gff_to_biosql.py

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Scripts/gff/gff_to_genbank.py

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Tests/GFF/F3-unique-3.v2.gff

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Tests/GFF/c_elegans_WS199_ann_gff.txt

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Tests/GFF/c_elegans_WS199_dna_shortened.fa

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Tests/GFF/c_elegans_WS199_shortened_gff.txt

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Tests/GFF/ensembl_gtf.txt

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Tests/GFF/glimmer_nokeyval.gff3

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Tests/GFF/hybrid1.gff3

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Tests/GFF/jgi_gff2.txt

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Tests/GFF/mouse_extra_comma.gff3

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Tests/GFF/ncbi_gff3.txt

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Tests/GFF/problem_sequence_region.gff3

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Tests/GFF/spaces.gff3

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Tests/GFF/trans_splicing.gff3

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Tests/GFF/transcripts.gff3

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Tests/GFF/unescaped-semicolon.gff3

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Tests/GFF/wormbase_gff2.txt

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Tests/GFF/wormbase_gff2_alt.txt

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<a href="#936fbcee4a35275ed493abce9f6c9e7f4180931b">

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Tests/test_GFFSeqIOFeatureAdder.py

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<a href="#788d776bfe907f02f738f7115e219184170cb4f7">

bcbio_gff.egg-info/PKG-INFO

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<a href="#944df03d39008ed8c63cac4c573db3e9218908ca">

bcbio_gff.egg-info/SOURCES.txt

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bcbio_gff.egg-info/requires.txt

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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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</ul>

<h4>Changes:</h4>

<li id="ba3404825a4d349f45211497986428bd4b75a757">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#ba3404825a4d349f45211497986428bd4b75a757"><strong>BCBio/GFF/GFFParser.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,8 +19,10 @@ import os</td>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">copy</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">io</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six.moves</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">urllib</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Make defaultdict compatible with versions of python older than 2.4</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,8 +36,10 @@ from Bio.SeqRecord import SeqRecord</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqFeature</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BiopythonDeprecationWarning</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="n" style="color: #333;">warnings</span><span class="p">.</span><span class="n" style="color: #333;">simplefilter</span><span class="p">(</span><span class="s" style="color: #d14;">"ignore"</span><span class="p">,</span> <span class="n" style="color: #333;">BiopythonDeprecationWarning</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>

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<pre style="margin: 0;"> <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;">_gff_line_map</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">    <span class="s" style="color: #d14;">"""Map part of Map-Reduce; parses a line of GFF into a dictionary.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,6 +50,7 @@ def _gff_line_map(line, params):</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;">        - determines the type of attribute (flat, parent, child or annotation)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;">        - generates a dictionary of GFF info which can be serialized as JSON</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_merge_keyvals</span><span class="p">(</span><span class="n" style="color: #333;">parts</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python">        <span class="s" style="color: #d14;">"""Merge key-values escaped by quotes that are improperly split at semicolons.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,6 +67,7 @@ def _gff_line_map(line, params):</td>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python">    <span class="n" style="color: #333;">gff3_kw_pat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">"\w+="</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_split_keyvals</span><span class="p">(</span><span class="n" style="color: #333;">keyval_str</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">        <span class="s" style="color: #d14;">"""Split key-value pairs in a GFF2, GTF and GFF3 compatible way.</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -151,15 +157,14 @@ def _gff_line_map(line, params):</td>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">                        <span class="n" style="color: #333;">gff_parts</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="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">][</span><span class="n" style="color: #333;">flat_name</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python">                        <span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</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="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="s" style="color: #d14;">"id"</span><span class="p">]]</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># children types</span></span>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="s" style="color: #d14;">"type"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"intron"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"three_prime_UTR"</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python">                        <span class="s" style="color: #d14;">"coding_exon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"five_prime_UTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stop_codon"</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python">                        <span class="s" style="color: #d14;">"start_codon"</span><span class="p">]:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="s" style="color: #d14;">"type"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"intron"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"three_prime_UTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">"coding_exon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"five_prime_UTR"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python">                                           <span class="s" style="color: #d14;">"stop_codon"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start_codon"</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">                    <span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</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="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="s" style="color: #d14;">"quals"</span><span class="p">][</span><span class="n" style="color: #333;">flat_name</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"></span>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gff_parts</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python">    <span class="n" style="color: #333;">strand_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'+'</span><span class="idiff left"> </span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">'-'</span><span class="idiff"> </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 class="s" style="color: #d14;">'?'</span><span class="idiff right"> </span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">    <span class="n" style="color: #333;">strand_map</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'+'</span><span class="p">:</span> <span class="mi" style="color: #099;">1</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;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">'?'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC168" 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;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC169" 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="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"##"</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[(</span><span class="s" style="color: #d14;">'directive'</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])]</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,8 +173,7 @@ def _gff_line_map(line, params):</td>

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<pre style="margin: 0;"> <span id="LC173" 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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<pre style="margin: 0;"> <span id="LC174" 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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<pre style="margin: 0;"> <span id="LC175" 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="n" style="color: #333;">items</span><span class="p">():</span></span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python">                <span class="n" style="color: #333;">cur_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;">-<span id="LC172" 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="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">                <span class="n" style="color: #333;">cur_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">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="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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<pre style="margin: 0;"> <span id="LC177" 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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<pre style="margin: 0;"> <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;">False</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">                    <span class="k" style="font-weight: 600;">break</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -200,8 +204,7 @@ def _gff_line_map(line, params):</td>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python">            <span class="n" style="color: #333;">gff_info</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;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># if we are describing a location, then we are a feature</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]:</span></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python">                <span class="n" style="color: #333;">gff_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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</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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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])]</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python">                <span class="n" style="color: #333;">gff_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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</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 class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])]</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python">                <span class="n" style="color: #333;">gff_info</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python">                <span class="n" style="color: #333;">gff_info</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="n" style="color: #333;">quals</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'ID'</span><span class="p">,</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>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python">                <span class="n" style="color: #333;">gff_info</span><span class="p">[</span><span class="s" style="color: #d14;">'strand'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strand_map</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">gff_parts</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">],</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -232,6 +235,7 @@ def _gff_line_map(line, params):</td>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="p">[(</span><span class="n" style="color: #333;">final_key</span><span class="p">,</span> <span class="n" style="color: #333;">gff_info</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>

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<td class="new_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_gff_line_reduce</span><span class="p">(</span><span class="n" style="color: #333;">map_results</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">    <span class="s" style="color: #d14;">"""Reduce part of Map-Reduce; combines results of parsed features.</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -248,6 +252,7 @@ def _gff_line_reduce(map_results, out, params):</td>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python">            <span class="n" style="color: #333;">vals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simplejson</span><span class="p">.</span><span class="n" style="color: #333;">dumps</span><span class="p">(</span><span class="n" style="color: #333;">vals</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python">        <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">vals</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_MultiIDRemapper</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">    <span class="s" style="color: #d14;">"""Provide an ID remapping for cases where a parent has a non-unique ID.</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -255,6 +260,7 @@ class _MultiIDRemapper:</td>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"><span class="s" style="color: #d14;">    by using the unique sequence region to assign children to the right</span></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"><span class="s" style="color: #d14;">    parent.</span></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC264" 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="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">base_id</span><span class="p">,</span> <span class="n" style="color: #333;">all_parents</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_base_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base_id</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parents</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_parents</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -271,9 +277,11 @@ class _MultiIDRemapper:</td>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if we haven't found a location match but parents are umabiguous, return that</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parents</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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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_base_id</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Did not find remapped ID location: %s, %s, %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_base_id</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="s" style="color: #d14;">'location'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parents</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python">                <span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'location'</span><span class="p">]))</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python">            <span class="s" style="color: #d14;">"Did not find remapped ID location: %s, %s, %s"</span> <span class="o" style="font-weight: 600;">%</span></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python">            <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_base_id</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="s" style="color: #d14;">'location'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parents</span><span class="p">],</span> <span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'location'</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_AbstractMapReduceGFF</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python">    <span class="s" style="color: #d14;">"""Base class providing general GFF parsing for local and remote classes.</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -283,6 +291,7 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;">    the _gff_process function, which returns a dictionary of SeqRecord</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"><span class="s" style="color: #d14;">    information.</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"></span>

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<pre style="margin: 0;"> <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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python">        <span class="s" style="color: #d14;">"""Initialize GFF parser </span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -311,8 +320,7 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC320" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">parse_in_parts</span><span class="p">(</span><span class="n" style="color: #333;">gff_files</span><span class="p">,</span> <span class="n" style="color: #333;">base_dict</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC321" 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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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_in_parts</span><span class="p">(</span><span class="bp" style="color: #999;">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;">base_dict</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;">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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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python">            <span class="n" style="color: #333;">target_lines</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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<pre style="margin: 0;">+<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;">parse_in_parts</span><span class="p">(</span><span class="bp" style="color: #999;">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;">base_dict</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;">limit_info</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;">target_lines</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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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">        <span class="s" style="color: #d14;">"""Parse a region of a GFF file specified, returning info as generated.</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"><span class="s" style="color: #d14;">        target_lines -- The number of lines in the file which should be used</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -363,8 +371,7 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python">        <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_annotations</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'annotation'</span><span class="p">,</span> <span class="p">[]))</span></span>

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<pre style="margin: 0;"> <span id="LC372" 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;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'feature'</span><span class="p">,</span> <span class="p">[]):</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">base</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_toplevel_feature</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python">        <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_parent_child_features</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'parent'</span><span class="p">,</span> <span class="p">[]),</span></span>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python">                <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'child'</span><span class="p">,</span> <span class="p">[]))</span></span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python">        <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_parent_child_features</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'parent'</span><span class="p">,</span> <span class="p">[]),</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'child'</span><span class="p">,</span> <span class="p">[]))</span></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python">        <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_seqs</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'fasta'</span><span class="p">,</span> <span class="p">[]))</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python">        <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_directives</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'directive'</span><span class="p">,</span> <span class="p">[]))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">base</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -384,8 +391,11 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python">                    <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">parts</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" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># specific directives that need special handling</span></span>

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<td class="old_line diff-line-num old" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"sequence-region"</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># convert to Python 0-based coordinates</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python">                    <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">val</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"sequence-region"</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># convert to Python 0-based coordinates</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">val</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 class="c1" style="color: #998; font-style: italic;"># handle regions missing contig</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python">                        <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">val</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python">                    <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">val</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python">                        <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">val</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python">                <span class="n" style="color: #333;">dir_keyvals</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">vals</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dir_keyvals</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC401" 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;">base</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">multi_remap</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python">                    <span class="n" style="color: #333;">pid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">multi_remap</span><span class="p">[</span><span class="n" style="color: #333;">pid</span><span class="p">].</span><span class="n" style="color: #333;">remap_id</span><span class="p">(</span><span class="n" style="color: #333;">child_dict</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python">                    <span class="n" style="color: #333;">child_feature</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="n" style="color: #333;">pindex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pid</span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python">                <span class="n" style="color: #333;">children_prep</span><span class="p">[</span><span class="n" style="color: #333;">pid</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">child_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python">                                           <span class="n" style="color: #333;">child_feature</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python">                <span class="n" style="color: #333;">children_prep</span><span class="p">[</span><span class="n" style="color: #333;">pid</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">child_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">],</span> <span class="n" style="color: #333;">child_feature</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python">        <span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">children_prep</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># add children to parents that exist</span></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cur_parent_dict</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parents</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">            <span class="n" style="color: #333;">cur_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_parent_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC432" 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;">in</span> <span class="n" style="color: #333;">multi_remap</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python">                <span class="n" style="color: #333;">cur_parent_dict</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="n" style="color: #333;">multi_remap</span><span class="p">[</span><span class="n" style="color: #333;">cur_id</span><span class="p">].</span><span class="n" style="color: #333;">remap_id</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python">                        <span class="n" style="color: #333;">cur_parent_dict</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python">                <span class="n" style="color: #333;">cur_parent_dict</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="n" style="color: #333;">multi_remap</span><span class="p">[</span><span class="n" style="color: #333;">cur_id</span><span class="p">].</span><span class="n" style="color: #333;">remap_id</span><span class="p">(</span><span class="n" style="color: #333;">cur_parent_dict</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python">            <span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_toplevel_feature</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">cur_parent_dict</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python">            <span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_children_to_parent</span><span class="p">(</span><span class="n" style="color: #333;">cur_parent</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python">                                                                <span class="n" style="color: #333;">children</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python">            <span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_children_to_parent</span><span class="p">(</span><span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">children</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># create parents for children without them (GFF2 or split/bad files)</span></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">children</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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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python">            <span class="n" style="color: #333;">parent_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_children</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">islice</span><span class="p">(</span><span class="n" style="color: #333;">children</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -433,15 +440,12 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cur_children</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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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python">                <span class="n" style="color: #333;">rec_id</span><span class="p">,</span> <span class="n" style="color: #333;">child</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_children</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python">                <span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">child</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="p">,</span> <span class="n" style="color: #333;">child</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="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python">                <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_rec</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python">                                          <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">rec_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rec_id</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loc</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python">                <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_rec</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">rec_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rec_id</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loc</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC444" 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="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">children</span><span class="p">[</span><span class="n" style="color: #333;">parent_id</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python">                <span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_missing_parent</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">parent_id</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python">                                                            <span class="n" style="color: #333;">cur_children</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python">                <span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_children_to_parent</span><span class="p">(</span><span class="n" style="color: #333;">cur_parent</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python">                                                                    <span class="n" style="color: #333;">children</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python">                <span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_missing_parent</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">parent_id</span><span class="p">,</span> <span class="n" style="color: #333;">cur_children</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python">                <span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">children</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_children_to_parent</span><span class="p">(</span><span class="n" style="color: #333;">cur_parent</span><span class="p">,</span> <span class="n" style="color: #333;">children</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">base</span></span>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_identify_dup_ids</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">parents</span><span class="p">):</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -454,8 +458,7 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python">        <span class="n" style="color: #333;">multi_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="p">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">parent</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parents</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python">            <span class="n" style="color: #333;">multi_ids</span><span class="p">[</span><span class="n" style="color: #333;">parent</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">]].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">parent</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC457" class="line" lang="python">        <span class="n" style="color: #333;">multi_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">ps</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">ps</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">multi_ids</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="python">                     <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">parents</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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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python">        <span class="n" style="color: #333;">multi_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">ps</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">ps</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">multi_ids</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">parents</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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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python">        <span class="n" style="color: #333;">multi_remap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">parents</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">multi_ids</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python">            <span class="n" style="color: #333;">multi_remap</span><span class="p">[</span><span class="n" style="color: #333;">mid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_MultiIDRemapper</span><span class="p">(</span><span class="n" style="color: #333;">mid</span><span class="p">,</span> <span class="n" style="color: #333;">parents</span><span class="p">)</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -525,13 +528,15 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python">        <span class="n" style="color: #333;">child_strands</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">strand</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur_children</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python">        <span class="n" style="color: #333;">inferred_strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">child_strands</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">child_strands</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">base_rec_id</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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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python">        <span class="n" style="color: #333;">feature_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</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;">parent_id</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">inferred_strand</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python">                            <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 class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">ID</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">parent_id</span><span class="p">]),</span></span>

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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python">                            <span class="n" style="color: #333;">rec_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">base_rec_id</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python">        <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">c</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="p">,</span> <span class="n" style="color: #333;">c</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="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python">                  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur_children</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python">        <span class="n" style="color: #333;">feature_dict</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="nb" style="color: #0086b3;">min</span><span class="p">([</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">coords</span><span class="p">]),</span></span>

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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python">                                    <span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">coords</span><span class="p">]))</span></span>

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python">        <span class="n" style="color: #333;">feature_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python">            <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">parent_id</span><span class="p">,</span></span>

</pre>

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533

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python">            <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">inferred_strand</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python">            <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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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python">            <span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">ID</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">parent_id</span><span class="p">]),</span></span>

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python">            <span class="n" style="color: #333;">rec_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">base_rec_id</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="python">        <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">c</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="p">,</span> <span class="n" style="color: #333;">c</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="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur_children</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python">        <span class="n" style="color: #333;">feature_dict</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="nb" style="color: #0086b3;">min</span><span class="p">([</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">coords</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">coords</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_toplevel_feature</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">feature_dict</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_toplevel_feature</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">feature_dict</span><span class="p">):</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -546,8 +551,9 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python">        <span class="s" style="color: #d14;">"""Retrieve a Biopython feature from our dictionary representation.</span></span>

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python">        <span class="n" style="color: #333;">location</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqFeature</span><span class="p">.</span><span class="n" style="color: #333;">FeatureLocation</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'location'</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python">        <span class="n" style="color: #333;">new_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqFeature</span><span class="p">.</span><span class="n" style="color: #333;">SeqFeature</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python">                <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'strand'</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python">        <span class="n" style="color: #333;">new_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqFeature</span><span class="p">.</span><span class="n" style="color: #333;">SeqFeature</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python">            <span class="n" style="color: #333;">location</span><span class="p">,</span> <span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</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;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">],</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">feature_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'strand'</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Support for Biopython 1.68 and above, which removed sub_features</span></span>

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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">new_feature</span><span class="p">,</span> <span class="s" style="color: #d14;">"sub_features"</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python">            <span class="n" style="color: #333;">new_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>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -559,9 +565,11 @@ class _AbstractMapReduceGFF:</td>

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_GFFParserLocalOut</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python">    <span class="s" style="color: #d14;">"""Provide a collector for local GFF MapReduce file parsing.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC573" 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="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">smart_breaks</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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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_items</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_smart_breaks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smart_breaks</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -619,13 +627,15 @@ class _GFFParserLocalOut:</td>

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_last_parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_items</span></span>

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GFFParser</span><span class="p">(</span><span class="n" style="color: #333;">_AbstractMapReduceGFF</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python">    <span class="s" style="color: #d14;">"""Local GFF parser providing standardized parsing of GFF3 and GFF2 files.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC635" 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="bp" style="color: #999;">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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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python">        <span class="n" style="color: #333;">_AbstractMapReduceGFF</span><span class="p">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python">        <span class="bp" style="color: #999;">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="new_line diff-line-num old" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC638" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC639" 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="bp" style="color: #999;">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="new_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python">        <span class="s" style="color: #d14;">"""Process GFF addition without any parallelization.</span></span>

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -655,40 +665,46 @@ class GFFParser(_AbstractMapReduceGFF):</td>

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">need_close</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python">                <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

657

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<td class="new_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

667

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_lines_to_out_info</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">line_iter</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC659" class="line" lang="python">            <span class="n" style="color: #333;">target_lines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_lines_to_out_info</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">line_iter</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 class="n" style="color: #333;">target_lines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python">        <span class="s" style="color: #d14;">"""Generate SeqRecord and SeqFeatures from GFF file lines.</span></span>

</pre>

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661

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<td class="new_line diff-line-num" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

670

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

662

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<td class="new_line diff-line-num" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python">        <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_examiner</span><span class="p">.</span><span class="n" style="color: #333;">_get_local_params</span><span class="p">(</span><span class="n" style="color: #333;">limit_info</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

663

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<td class="new_line diff-line-num old" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python">        <span class="n" style="color: #333;">out_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

664

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<td class="new_line diff-line-num old" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC664" 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python">        <span class="n" style="color: #333;">out_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_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 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

665

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<td class="new_line diff-line-num" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

673

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<pre style="margin: 0;"> <span id="LC673" 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;">False</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

666

</td>

<td class="new_line diff-line-num" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

674

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<pre style="margin: 0;"> <span id="LC674" 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;">line_iter</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

667

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<td class="new_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC675" class="line" lang="python">            <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_map_fn</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

668

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<td class="new_line diff-line-num" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

676

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_line_adjust_fn</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">results</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

669

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<td class="new_line diff-line-num" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</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="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'directive'</span><span class="p">]:</span></span>

</pre>

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670

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<pre style="margin: 0;">-<span id="LC670" class="line" lang="python">                    <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</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>

</pre>

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671

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<td class="new_line diff-line-num old" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python">                        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_line_adjust_fn</span><span class="p">(</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;">1</span><span class="p">]))]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python">                    <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_line_adjust_fn</span><span class="p">(</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;">1</span><span class="p">]))]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC679" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reduce_fn</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">,</span> <span class="n" style="color: #333;">out_info</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC673" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">target_lines</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">out_info</span><span class="p">.</span><span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_lines</span> <span class="ow" style="font-weight: 600;">and</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC674" class="line" lang="python">                    <span class="n" style="color: #333;">out_info</span><span class="p">.</span><span class="n" style="color: #333;">can_break</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">target_lines</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">out_info</span><span class="p">.</span><span class="n" style="color: #333;">num_lines</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">target_lines</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">out_info</span><span class="p">.</span><span class="n" style="color: #333;">can_break</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC681" 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="n" style="color: #333;">get_results</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python">                <span class="n" style="color: #333;">out_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_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>

</pre>

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677

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<td class="new_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC677" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC678" class="line" lang="python">            <span class="k" style="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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

679

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<td class="new_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC679" 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

682

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python">                <span class="n" style="color: #333;">out_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_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 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

683

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC683" class="line" lang="python">            <span class="k" style="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="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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC684" 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>

</pre>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC685" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

682

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<td class="new_line diff-line-num" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

686

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC686" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

683

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<td class="new_line diff-line-num" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

687

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC687" class="line" lang="python">        <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FakeHandle</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

688

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC688" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

684

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<td class="new_line diff-line-num" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">line_iter</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

685

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<td class="new_line diff-line-num" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

690

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC690" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_iter</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

691

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC691" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC692" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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687

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<td class="new_line diff-line-num" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC693" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

694

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC694" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC695" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__next__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

689

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<td class="new_line diff-line-num" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

696

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC696" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iter</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

690

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<td class="new_line diff-line-num old" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC690" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

691

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<td class="new_line diff-line-num old" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC691" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iter</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

697

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC697" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC698" class="line" lang="python">            <span class="nb" style="color: #0086b3;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__next__</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC699" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

700

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC700" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

701

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC701" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iter</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC703" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span>  <span class="c1" style="color: #998; font-style: italic;"># Used by Biopython to sniff unicode vs bytes</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python">                    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readline</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python">                    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_iter</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -701,9 +717,11 @@ class GFFParser(_AbstractMapReduceGFF):</td>

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">out_info</span><span class="p">.</span><span class="n" style="color: #333;">has_items</span><span class="p">():</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC718" 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="n" style="color: #333;">get_results</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

720

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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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<td class="new_line diff-line-num" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DiscoGFFParser</span><span class="p">(</span><span class="n" style="color: #333;">_AbstractMapReduceGFF</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<td class="new_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python">    <span class="s" style="color: #d14;">"""GFF Parser with parallelization through Disco (http://discoproject.org.</span></span>

</pre>

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706

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<td class="new_line diff-line-num" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC724" class="line" lang="python"></span>

</pre>

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707

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<td class="new_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

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<pre style="margin: 0;"> <span id="LC725" 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="bp" style="color: #999;">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>

</pre>

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708

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<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">        <span class="s" style="color: #d14;">"""Initialize parser.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="new_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"><span class="s" style="color: #d14;">        </span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -720,32 +738,36 @@ class DiscoGFFParser(_AbstractMapReduceGFF):</td>

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<td class="old_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

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<td class="new_line diff-line-num" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

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<pre style="margin: 0;"> <span id="LC738" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

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<td class="new_line diff-line-num" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python">        <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

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<td class="new_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC740" class="line" lang="python">        <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">disco</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

723

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<td class="new_line diff-line-num old" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC723" 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"> </span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

741

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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># absolute path names unless they are special disco files</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

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<td class="new_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

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<pre style="margin: 0;"> <span id="LC742" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

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<td class="new_line diff-line-num" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

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<pre style="margin: 0;"> <span id="LC743" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

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<td class="new_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

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<pre style="margin: 0;"> <span id="LC744" 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="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC745" class="line" lang="python">                <span class="n" style="color: #333;">full_files</span><span class="p">.</span><span class="n" style="color: #333;">append</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="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

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<td class="new_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

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<td class="new_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC747" class="line" lang="python">                <span class="n" style="color: #333;">full_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

730

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC730" class="line" lang="python">        <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">disco</span><span class="p">.</span><span class="n" style="color: #333;">job</span><span class="p">(</span><span class="bp" style="color: #999;">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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gff_reader"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

731

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC731" class="line" lang="python">                <span class="nb" style="color: #0086b3;">input</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">full_files</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

732

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC732" class="line" lang="python">                <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">disco</span><span class="p">.</span><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 class="p">,</span> <span class="n" style="color: #333;">jsonify</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

733

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC733" class="line" lang="python">                    <span class="n" style="color: #333;">filter_info</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_examiner</span><span class="p">.</span><span class="n" style="color: #333;">_filter_info</span><span class="p">),</span></span>

</pre>

</td>

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734

</td>

<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC734" class="line" lang="python">                <span class="n" style="color: #333;">required_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"simplejson"</span><span class="p">,</span> <span class="s" style="color: #d14;">"collections"</span><span class="p">,</span> <span class="s" style="color: #d14;">"re"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

735

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<td class="new_line diff-line-num old" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC735" class="line" lang="python">                <span class="nb" style="color: #0086b3;">map</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_map_fn</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">reduce</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reduce_fn</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

748

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<pre style="margin: 0;">+<span id="LC748" class="line" lang="python">        <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">disco</span><span class="p">.</span><span class="n" style="color: #333;">job</span><span class="p">(</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

749

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC749" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_disco_host</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC750" class="line" lang="python">            <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gff_reader"</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

751

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC751" class="line" lang="python">            <span class="nb" style="color: #0086b3;">input</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">full_files</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC752" class="line" lang="python">            <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">disco</span><span class="p">.</span><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 class="p">,</span> <span class="n" style="color: #333;">jsonify</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">filter_info</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_examiner</span><span class="p">.</span><span class="n" style="color: #333;">_filter_info</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC753" class="line" lang="python">            <span class="n" style="color: #333;">required_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"simplejson"</span><span class="p">,</span> <span class="s" style="color: #d14;">"collections"</span><span class="p">,</span> <span class="s" style="color: #d14;">"re"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

754

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC754" class="line" lang="python">            <span class="nb" style="color: #0086b3;">map</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_map_fn</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

755

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC755" class="line" lang="python">            <span class="nb" style="color: #0086b3;">reduce</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reduce_fn</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

756

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC756" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

</td>

<td class="new_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC757" class="line" lang="python">        <span class="n" style="color: #333;">processed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

<td class="new_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC758" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">out_key</span><span class="p">,</span> <span class="n" style="color: #333;">out_val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">disco</span><span class="p">.</span><span class="n" style="color: #333;">result_iterator</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

</td>

<td class="new_line diff-line-num" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

759

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC759" class="line" lang="python">            <span class="n" style="color: #333;">processed</span><span class="p">[</span><span class="n" style="color: #333;">out_key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">simplejson</span><span class="p">.</span><span class="n" style="color: #333;">loads</span><span class="p">(</span><span class="n" style="color: #333;">out_val</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

</td>

<td class="new_line diff-line-num" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

760

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC760" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">processed</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

</td>

<td class="new_line diff-line-num" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

761

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC761" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

762

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC762" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="new_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

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<pre style="margin: 0;"> <span id="LC763" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">gff_files</span><span class="p">,</span> <span class="n" style="color: #333;">base_dict</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;">limit_info</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;">target_lines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

</td>

<td class="new_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

764

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<pre style="margin: 0;"> <span id="LC764" class="line" lang="python">    <span class="s" style="color: #d14;">"""High level interface to parse GFF files into SeqRecords and SeqFeatures.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

<td class="new_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

765

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC765" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

</td>

<td class="new_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

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<pre style="margin: 0;"> <span id="LC766" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

745

</td>

<td class="new_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC745" 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="n" style="color: #333;">parse_in_parts</span><span class="p">(</span><span class="n" style="color: #333;">gff_files</span><span class="p">,</span> <span class="n" style="color: #333;">base_dict</span><span class="p">,</span> <span class="n" style="color: #333;">limit_info</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

746

</td>

<td class="new_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC746" class="line" lang="python">            <span class="n" style="color: #333;">target_lines</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

767

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC767" 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="n" style="color: #333;">parse_in_parts</span><span class="p">(</span><span class="n" style="color: #333;">gff_files</span><span class="p">,</span> <span class="n" style="color: #333;">base_dict</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>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

</td>

<td class="new_line diff-line-num" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

768

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC768" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">rec</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

</td>

<td class="new_line diff-line-num" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

769

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

770

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

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<td class="new_line diff-line-num" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_simple</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="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

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<td class="new_line diff-line-num" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

772

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC772" class="line" lang="python">    <span class="s" style="color: #d14;">"""Parse GFF files as line by line dictionary of parts.</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

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<td class="new_line diff-line-num" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

773

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -756,18 +778,24 @@ def parse_simple(gff_files, limit_info=None):</td>

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<td class="old_line diff-line-num" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

</td>

<td class="new_line diff-line-num" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

778

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC778" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">rec</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>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

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<td class="new_line diff-line-num" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC779" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"parent"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

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<td class="new_line diff-line-num" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC780" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="s" style="color: #d14;">"parent"</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

781

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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"feature"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

782

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC782" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">rec</span><span class="p">[</span><span class="s" style="color: #d14;">"feature"</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

759

</td>

<td class="new_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC783" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># ignore directive lines</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

760

</td>

<td class="new_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC784" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

761

</td>

<td class="new_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC785" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"directive"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rec</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

</td>

<td class="new_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC787" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

</td>

<td class="new_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_file_or_handle</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

764

</td>

<td class="new_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC789" class="line" lang="python">    <span class="s" style="color: #d14;">"""Decorator to handle either an input handle or a file.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

765

</td>

<td class="new_line diff-line-num" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC791" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

</td>

<td class="new_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC792" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_file_or_handle_inside</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>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

</td>

<td class="new_line diff-line-num" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

793

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC793" class="line" lang="python">        <span class="n" style="color: #333;">in_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

768

</td>

<td class="new_line diff-line-num" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

794

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC794" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"read"</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

769

</td>

<td class="new_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

795

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC795" class="line" lang="python">            <span class="n" style="color: #333;">need_close</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

770

</td>

<td class="new_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC796" class="line" lang="python">            <span class="n" style="color: #333;">in_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">in_file</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

797

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC797" 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;">PY3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">,</span> <span class="n" style="color: #333;">io</span><span class="p">.</span><span class="n" style="color: #333;">TextIOBase</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

798

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC798" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span><span class="s" style="color: #d14;">'input handle must be opened in text mode'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

</td>

<td class="new_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC799" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

772

</td>

<td class="new_line diff-line-num" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC800" class="line" lang="python">            <span class="n" style="color: #333;">need_close</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

</td>

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<td class="new_line diff-line-num" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python">            <span class="n" style="color: #333;">in_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">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="diff-line-num unfold js-unfold old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -776,8 +804,10 @@ def _file_or_handle(fn):</td>

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<td class="old_line diff-line-num" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

776

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<td class="new_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC804" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">need_close</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

777

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<td class="new_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python">            <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

778

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<td class="new_line diff-line-num" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

806

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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

807

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

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<td class="new_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC808" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_file_or_handle_inside</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

810

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<pre style="margin: 0;">+<span id="LC810" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

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<td class="new_line diff-line-num" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

811

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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GFFExaminer</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

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<td class="new_line diff-line-num" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

812

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<pre style="margin: 0;"> <span id="LC812" class="line" lang="python">    <span class="s" style="color: #d14;">"""Provide high level details about a GFF file to refine parsing.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<td class="new_line diff-line-num" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -787,19 +817,22 @@ class GFFExaminer:</td>

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<td class="old_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

787

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<td class="new_line diff-line-num" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

817

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<pre style="margin: 0;"> <span id="LC817" class="line" lang="python"><span class="s" style="color: #d14;">    information you need. This class provides high level summary details to</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

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<td class="new_line diff-line-num" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC818" class="line" lang="python"><span class="s" style="color: #d14;">    help in learning.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

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<td class="new_line diff-line-num" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

820

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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

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<td class="new_line diff-line-num" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

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<pre style="margin: 0;"> <span id="LC821" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

791

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<td class="new_line diff-line-num old" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC791" class="line" lang="python">        <span class="bp" style="color: #999;">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="nb" style="color: #0086b3;">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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

792

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<td class="new_line diff-line-num old" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC792" 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>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

793

</td>

<td class="new_line diff-line-num old" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC793" class="line" lang="python">    </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

822

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC822" class="line" lang="python">        <span class="bp" style="color: #999;">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="nb" style="color: #0086b3;">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 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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

823

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC823" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

794

</td>

<td class="new_line diff-line-num" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

824

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC824" 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="bp" style="color: #999;">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>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

825

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC825" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

795

</td>

<td class="new_line diff-line-num" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

826

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC826" 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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

827

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC827" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

</td>

<td class="new_line diff-line-num" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC828" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

</td>

<td class="new_line diff-line-num" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC829" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jsonify</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

830

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC830" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

</td>

<td class="new_line diff-line-num" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

831

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC831" class="line" lang="python">        <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_LocalParams</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="new_line diff-line-num" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC832" 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>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

</td>

<td class="new_line diff-line-num" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC833" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_filter_info</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

801

</td>

<td class="new_line diff-line-num" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC834" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">params</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

802

</td>

<td class="new_line diff-line-num old" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC802" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

835

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC835" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

803

</td>

<td class="new_line diff-line-num" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC836" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">_file_or_handle</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

</td>

<td class="new_line diff-line-num" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC837" 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="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">gff_handle</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

805

</td>

<td class="new_line diff-line-num" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC838" 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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -856,16 +889,12 @@ class GFFExaminer:</td>

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<pre style="margin: 0;"> <span id="LC889" 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="n" style="color: #333;">startswith</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" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC890" 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" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC891" 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="n" style="color: #333;">strip</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">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="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC859" class="line" lang="python">                <span class="n" style="color: #333;">line_type</span><span class="p">,</span> <span class="n" style="color: #333;">line_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_gff_line_map</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC860" class="line" lang="python">                        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_local_params</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="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'parent'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">line_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'child'</span> <span class="ow" style="font-weight: 600;">and</span></span>

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<td class="old_line diff-line-num old" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python">                        <span class="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">])):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python">                    <span class="n" style="color: #333;">parent_sts</span><span class="p">[</span><span class="n" style="color: #333;">line_info</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python">                            <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="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'source'</span><span class="p">,</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="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python">                <span class="n" style="color: #333;">line_type</span><span class="p">,</span> <span class="n" style="color: #333;">line_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_gff_line_map</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_local_params</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC893" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'parent'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">line_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'child'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">])):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC894" class="line" lang="python">                    <span class="n" style="color: #333;">parent_sts</span><span class="p">[</span><span class="n" style="color: #333;">line_info</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="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="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'source'</span><span class="p">,</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="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">])</span></span>

</pre>

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865

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<td class="new_line diff-line-num" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC895" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'child'</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC896" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">parent_id</span> <span class="ow" style="font-weight: 600;">in</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;">'Parent'</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC867" class="line" lang="python">                        <span class="n" style="color: #333;">child_sts</span><span class="p">[</span><span class="n" style="color: #333;">parent_id</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">((</span></span>

</pre>

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868

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<pre style="margin: 0;">-<span id="LC868" class="line" lang="python">                            <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="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'source'</span><span class="p">,</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="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python">                        <span class="n" style="color: #333;">child_sts</span><span class="p">[</span><span class="n" style="color: #333;">parent_id</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">((</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="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'source'</span><span class="p">,</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="n" style="color: #333;">line_info</span><span class="p">[</span><span class="s" style="color: #d14;">'type'</span><span class="p">]))</span></span>

</pre>

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869

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898

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<pre style="margin: 0;"> <span id="LC898" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#print parent_sts, child_sts</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

870

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<pre style="margin: 0;"> <span id="LC899" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># generate a dictionary of the unique final type relationships</span></span>

</pre>

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871

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<pre style="margin: 0;"> <span id="LC900" 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;">collections</span><span class="p">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="377317303b32a87f51356a964b30d05b7cf78ba3">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#377317303b32a87f51356a964b30d05b7cf78ba3"><strong>BCBio/GFF/__init__.py</strong></a>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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>

</pre>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__version__</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="s" style="color: #d14;">"0.6.<span class="idiff right">6</span>"</span></span></pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__version__</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;">"0.6.<span class="idiff right">7</span>"</span></span></pre>

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<br>

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<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>

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1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.0</span>

</pre>

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2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: bcbio-gff</span>

</pre>

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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(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.6.<span class="idiff left right">6</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.6.<span class="idiff left right">7</span></span>

</pre>

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4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Read and write Generic Feature Format (GFF) with Biopython integration.</span>

</pre>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/chapmanb/bcbb/tree/master/gff</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Brad Chapman</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: chapmanb@50mail.com</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="new_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">UNKNOWN</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">Biopython License</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Description: UNKNOWN</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Platform: UNKNOWN</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="05ff4d05b4718a5c1e7de6afef599c230c721357">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#05ff4d05b4718a5c1e7de6afef599c230c721357"><strong>Scripts/gff/access_gff_index.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">Requires:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">Index time:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">  44 Mb file</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">  11 seconds</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">  Index is 7.5Mb</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">with_statement</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bx</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">interval_index_file</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">gff_index</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">        <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">gff_file</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFExaminer</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#print exam.available_limits(gff_file)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">                <span class="s" style="color: #d14;">"three_prime_UTR"</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">            <span class="n" style="color: #333;">limit_info</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">    <span class="s" style="color: #d14;">"""Provide indexed access to a GFF file.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">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="n" style="color: #333;">keys</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parser</span><span class="p">.</span><span class="n" style="color: #333;">_normalize_limit_info</span><span class="p">(</span><span class="n" style="color: #333;">limit_info</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_as_iterator</span><span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parser</span><span class="p">.</span><span class="n" style="color: #333;">_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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_parser</span><span class="p">.</span><span class="n" style="color: #333;">_results_to_features</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(),</span> <span class="n" style="color: #333;">results</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<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="bp" style="color: #999;">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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<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="n" style="color: #333;">readline</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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<pre style="margin: 0;">+<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="n" style="color: #333;">Indexes</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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<pre style="margin: 0;">+<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="n" style="color: #333;">tell</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">readline</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">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="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">                <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">seqid</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">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="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python">        <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">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="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python">    <span class="n" style="color: #333;">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>

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<br>

</li>

<li id="41731cf6f4dd9bb65e654cdbac1505e47ccb8f13">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#41731cf6f4dd9bb65e654cdbac1505e47ccb8f13"><strong>Scripts/gff/genbank_to_gff.py</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Convert a GenBank file into GFF format.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">    genbank_to_gff.py <genbank_file></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

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15

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">        <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="n" style="color: #333;">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>

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<br>

</li>

<li id="2886ed2cda7201b9be162bae766fb9ce71abbc0d">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#2886ed2cda7201b9be162bae766fb9ce71abbc0d"><strong>Scripts/gff/gff2_to_gff3.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">    gff2_to_gff3.py <in_gff2_file></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">in_file</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFF3Writer</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">reader</span><span class="p">.</span><span class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">            <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">    <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">    <span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="n" style="color: #333;">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>

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<br>

</li>

<li id="ffc65bbac955d1dfd401d64cad0a8512786eeafd">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#ffc65bbac955d1dfd401d64cad0a8512786eeafd"><strong>Scripts/gff/gff_to_biosql.py</strong></a>

<hr>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">up. See:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">http://biopython.org/wiki/BioSQL</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">    set global max_allowed_packet=1000000000;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">    set global net_buffer_length=1000000;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">    gff_to_biosql.py <fasta file> <gff file></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__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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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">BioSQL</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BioSeqDatabase</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># -- To be customized</span></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># --</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">keys</span><span class="p">():</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python">            <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="n" style="color: #333;">new_database</span><span class="p">(</span><span class="n" style="color: #333;">biodb_name</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">            <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="n" style="color: #333;">remove_database</span><span class="p">(</span><span class="n" style="color: #333;">biodb_name</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">commit</span><span class="p">()</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">            <span class="n" style="color: #333;">server</span><span class="p">.</span><span class="n" style="color: #333;">new_database</span><span class="p">(</span><span class="n" style="color: #333;">biodb_name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">        <span class="n" style="color: #333;">db</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">commit</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">rollback</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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74

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>

</pre>

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76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">    <span class="n" style="color: #333;">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>

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<br>

</li>

<li id="1f1f2724f86460cdf01eaf8c32d97cf05f74f121">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#1f1f2724f86460cdf01eaf8c32d97cf05f74f121"><strong>Scripts/gff/gff_to_genbank.py</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<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>

</pre>

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3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

</td>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Usage:</span></span>

</pre>

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5

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<pre style="margin: 0;">+<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>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>

</pre>

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7

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">   are in the GFF</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">    <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">_check_gff</span><span class="p">(</span><span class="n" style="color: #333;">_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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">            <span class="k" style="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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">_flatten_features</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;">    everything top level.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

63

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<pre style="margin: 0;">+<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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

64

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">                <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">curf</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

66

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">                    <span class="n" style="color: #333;">nextf</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">    <span class="n" style="color: #333;">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>

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<br>

</li>

<li id="0f40c25b1a1324c08d8f7a1cf332d7006641fbca">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#0f40c25b1a1324c08d8f7a1cf332d7006641fbca"><strong>Tests/GFF/F3-unique-3.v2.gff</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##solid-gff-version 0.2</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##gff-version 2</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##source-version MaToGff.java v1.5</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##date 2008-05-28</span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##time 13:11:03</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##Type solid_read</span>

</pre>

</td>

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7

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">##primer-base F3=T</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">##max-num-mismatches 3</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">##max-read-length 20</span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">##line-order fragment</span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">##hdr seqname        source  feature start   end     score   strand  frame   [attributes]    [comments]</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">3_336_815_F3 solid   read    55409   55428   10.4    +       .       g=A3233312322232122211;i=1;p=1.000;q=23,12,18,17,10,24,19,14,27,9,23,9,16,20,11,7,8,4,4,14;u=0,0,0,1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">3_142_1011_F3        solid   read    91290   91309   5.0     -       .       g=T0330222333132222222;i=1;p=1.000;q=4,4,14,4,4,4,4,21,4,4,4,4,25,4,4,4,5,21,4,4;u=0,0,0,1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">3_341_424_F3 solid   read    102717  102736  10.6    -       .       g=T2203031313223113212;i=1;p=1.000;q=9,27,25,16,18,9,27,26,23,13,14,25,27,5,24,5,26,26,4,5;u=0,0,1</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">3_6_37_F3    solid   read    181053  181072  9.4     +       .       g=C3220221332111020310;i=1;p=1.000;q=9,5,13,9,10,22,6,12,21,7,13,4,21,16,23,6,20,20,13,6;u=0,0,0,1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">3_34_202_F3  solid   read    284207  284226  6.9     +       .       g=G0301333332232122333;i=1;p=1.000;q=6,15,21,8,12,4,4,5,12,8,4,12,4,7,10,6,8,16,4,6;u=0,1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">3_277_712_F3 solid   read    304136  304155  11.8    -       .       g=A2033101122223322133;i=1;p=1.000;q=26,11,14,27,4,17,4,26,26,23,17,25,26,27,21,23,5,20,26,23;u=0,1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">3_394_71_F3  solid   read    308736  308755  10.8    +       .       g=T3203322323203312331;i=1;p=1.000;q=9,24,19,15,20,18,20,10,13,13,11,21,12,7,4,11,20,24,4,25;u=0,1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">3_285_1497_F3        solid   read    404055  404074  8.4     -       .       g=T1221231003202232221;i=1;p=1.000;q=8,10,6,25,16,14,23,27,8,14,21,19,5,4,4,6,22,12,4,6;u=0,0,0,1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">3_228_178_F3 solid   read    453227  453246  9.5     -       .       g=G1130333332331110323;i=1;p=1.000;q=4,19,25,18,18,5,19,6,8,24,4,26,21,11,15,4,26,13,13,15;u=0,0,0,1</span>

</pre>

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127

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

128

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"># Elapsed time 0.846 secs</span></pre>

</td>

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<br>

</li>

<li id="455598c9a26aecd6f54c537a558d530222fe275a">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#455598c9a26aecd6f54c537a558d530222fe275a"><strong>Tests/GFF/c_elegans_WS199_ann_gff.txt</strong></a>

<hr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># modified GFF file to remove location coordinates and test annotations</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">I     Expr_profile    experimental_result_region      .       .       .       +       .       expr_profile=B0019.1</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="fe28203b812c0499b74f4922332eca3744fec114">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#fe28203b812c0499b74f4922332eca3744fec114"><strong>Tests/GFF/c_elegans_WS199_dna_shortened.fa</strong></a>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>I</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">gcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaa</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">gcctaagcctaagcctaagcctaagcctaagcctaagcct</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">>II</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">cctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaag</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">cctaagcctaagcctaagcctaagcctaagcctaagccta</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">>III</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">cctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaag</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">cctaagcctaagcctaagcctaagcctaagcctaagccta</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">>IV</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">cctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaag</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">cctaagcctaagcctaagcctaagcctaagcctaagccta</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">>V</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">gaattcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">ctaagcctaagcctaagcctaagcctaagcctaagcctaa</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">>X</span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">ctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagcctaagc</span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">ctaagcctaagcctaagcctaagcctaagcctaagcctaa</span>

</pre>

</td>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">>MtDNA</span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">cagtaaatagtttaataaaaatatagcatttgggttgctaagatattattactgatagaa</span>

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">tttttagtttaatttagaatgtatcacttacaatgatggg</span></pre>

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<br>

</li>

<li id="82717fa145804b249abb52d06924da7668cf62e4">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#82717fa145804b249abb52d06924da7668cf62e4"><strong>Tests/GFF/c_elegans_WS199_shortened_gff.txt</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">I     Orfeome PCR_product     12759747        12764936        .       -       .       amplified=1;pcr_product=mv_B0019.1</span>

</pre>

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2

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<pre style="margin: 0;">+<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>

</pre>

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3

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<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>

</pre>

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5

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<pre style="margin: 0;">+<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>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">I     Expr_profile    experimental_result_region      12762449        12764118        .       +       .       expr_profile=B0019.1</span>

</pre>

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7

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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21

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">I    history CDS     12759745        12759828        .       -       0       ID=CDS:B0019.1:wp173</span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">I    history CDS     12760365        12760494        .       -       0       ID=CDS:B0019.1:wp173</span>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">I    history CDS     12760834        12760904        .       -       2       ID=CDS:B0019.1:wp173</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">I    history CDS     12761172        12761516        .       -       2       ID=CDS:B0019.1:wp173</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">I    history CDS     12761577        12761626        .       -       1       ID=CDS:B0019.1:wp173</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">I    history CDS     12761795        12761953        .       -       1       ID=CDS:B0019.1:wp173</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">I    history CDS     12762127        12762268        .       -       2       ID=CDS:B0019.1:wp173</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">I    history CDS     12762648        12762806        .       -       2       ID=CDS:B0019.1:wp173</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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 new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">I    history CDS     12763448        12763655        .       -       0       ID=CDS:B0019.1:wp173</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">I    history CDS     12763729        12763882        .       -       1       ID=CDS:B0019.1:wp173</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">I    history CDS     12763979        12764102        .       -       2       ID=CDS:B0019.1:wp173</span>

</pre>

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</tr>

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">I    history CDS     12764291        12764471        .       -       0       ID=CDS:B0019.1:wp173</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">I    history CDS     12764812        12764937        .       -       0       ID=CDS:B0019.1:wp173</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">I    history CDS     12759745        12759828        .       -       0       ID=CDS:B0019.1:wp90</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

39

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">I    history CDS     12759949        12760013        .       -       2       ID=CDS:B0019.1:wp90</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">I    history CDS     12760227        12760319        .       -       2       ID=CDS:B0019.1:wp90</span>

</pre>

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</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">I    history CDS     12761172        12761516        .       -       2       ID=CDS:B0019.1:wp90</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">I    history CDS     12761577        12761626        .       -       1       ID=CDS:B0019.1:wp90</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">I    history CDS     12761795        12761953        .       -       1       ID=CDS:B0019.1:wp90</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">I    history CDS     12762127        12762268        .       -       2       ID=CDS:B0019.1:wp90</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">I    history CDS     12762648        12762806        .       -       2       ID=CDS:B0019.1:wp90</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">I    history CDS     12763112        12763249        .       -       2       ID=CDS:B0019.1:wp90</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">I    history CDS     12763469        12763655        .       -       0       ID=CDS:B0019.1:wp90</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

48

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">I    history CDS     12763729        12763882        .       -       1       ID=CDS:B0019.1:wp90</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">I    history CDS     12763979        12764102        .       -       2       ID=CDS:B0019.1:wp90</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">I    history CDS     12764291        12764471        .       -       0       ID=CDS:B0019.1:wp90</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">I    history CDS     12764812        12764937        .       -       0       ID=CDS:B0019.1:wp90</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

52

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">I    Oligo_set       reagent 12759745        12761589        .       -       .       oligo_set=Aff_B0019.1</span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">I    Coding_transcript       exon    12759745        12759828        .       -       0       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">I    Coding_transcript       exon    12759949        12760013        .       -       2       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">I    Coding_transcript       exon    12760227        12760319        .       -       2       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">I    Coding_transcript       exon    12760365        12760494        .       -       0       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">I    Coding_transcript       exon    12760834        12760904        .       -       2       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">I    Coding_transcript       exon    12761172        12761516        .       -       2       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">I    Coding_transcript       exon    12761799        12761953        .       -       1       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">I    Coding_transcript       exon    12762127        12762268        .       -       2       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">I    Coding_transcript       exon    12762648        12762806        .       -       2       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">I    Coding_transcript       exon    12763112        12763249        .       -       2       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">I    Coding_transcript       exon    12763448        12763655        .       -       0       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">I    Coding_transcript       exon    12763729        12763882        .       -       1       Parent=Transcript:B0019.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">I    Coding_transcript       three_prime_UTR 12759582        12759744        .       -       .       Parent=Transcript:B0019.1</span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">I    Promoterome     PCR_product     12764938        12766937        .       +       .       pcr_product=p_B0019.1_93</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">I    GenePair_STS    PCR_product     12762449        12764118        .       +       .       pcr_product=sjj_B0019.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">I    Coding_transcript       gene    12759582        12764949        .       -       .       ID=Gene:WBGene00000138</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">III  Orfeome PCR_product     13780230        13780850        .       +       .       amplified=1;pcr_product=mv_3R5.1.v6</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">IV   Orfeome PCR_product     17486939        17488952        .       -       .       amplified=1;pcr_product=mv_4R79.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">IV   Orfeome PCR_product     17480353        17483284        .       -       .       amplified=1;pcr_product=mv_4R79.2</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">X    Orfeome PCR_product     17714881        17718531        .       +       .       amplified=1;pcr_product=mv_6R55.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">X    Orfeome PCR_product     17712787        17714742        .       +       .       amplified=1;pcr_product=mv_6R55.2</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">II   Orfeome PCR_product     6995874 7010146 .       +       .       amplified=1;pcr_product=mv_AAA03517</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">III  Orfeome PCR_product     5625097 5631795 .       +       .       amplified=1;pcr_product=mv_AAA03544</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">X   GenePair_STS    PCR_product     9962853 9963737 .       +       .       pcr_product=cenix:102-c3</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">II  GenePair_STS    PCR_product     5507236 5508135 .       +       .       pcr_product=cenix:102-c4</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">V   GenePair_STS    PCR_product     10117842        10118735        .       +       .       pcr_product=cenix:102-c5</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">IV  GenePair_STS    PCR_product     3566130 3567025 .       +       .       pcr_product=cenix:102-c6</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">X   GenePair_STS    PCR_product     6117180 6117930 .       +       .       pcr_product=cenix:102-c7</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">IV  GenePair_STS    PCR_product     7189492 7190369 .       +       .       pcr_product=cenix:102-c9</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">II  GenePair_STS    PCR_product     14462527        14463202        .       +       .       pcr_product=cenix:102-d1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">X   Promoterome     PCR_product     2258069 2259336 .       +       .       pcr_product=p_AH9.2_93</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">IV  Promoterome     PCR_product     12157449        12159448        .       +       .       pcr_product=p_B0001.6_93</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">I   Promoterome     PCR_product     12764938        12766937        .       +       .       pcr_product=p_B0019.1_93</span>

</pre>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">V   Promoterome     PCR_product     10320122        10320689        .       +       .       pcr_product=p_B0024.12_93</span>

</pre>

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</tr>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">I   Coding_transcript       exon    4581214 4581237 .       -       0       Parent=Transcript:D1007.5b.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">I   Coding_transcript       exon    4581664 4582026 .       -       0       Parent=Transcript:D1007.5b.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">I   Coding_transcript       exon    4582412 4582718 .       -       1       Parent=Transcript:D1007.5b.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">I   Coding_transcript       exon    4583190 4583374 .       -       0       Parent=Transcript:D1007.5b.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">I   Coding_transcript       exon    4583426 4583509 .       -       0       Parent=Transcript:D1007.5b.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">I   Coding_transcript       exon    4583560 4583805 .       -       0       Parent=Transcript:D1007.5b.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">I   Coding_transcript       five_prime_UTR  4583806 4583815 .       -       .       Parent=Transcript:D1007.5b.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">I   Coding_transcript       three_prime_UTR 4580734 4581213 .       -       .       Parent=Transcript:D1007.5b.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">I   Coding_transcript       intron  4582027 4582411 .       -       .       Parent=Transcript:D1007.5b.1;confirmed_est=EB994038</span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">I   Coding_transcript       exon    4581214 4581237 .       -       0       Parent=Transcript:D1007.5b.2</span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">I   Coding_transcript       exon    4581664 4582026 .       -       0       Parent=Transcript:D1007.5b.2</span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">I   Coding_transcript       exon    4582412 4582718 .       -       1       Parent=Transcript:D1007.5b.2</span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">I   Coding_transcript       exon    4583190 4583374 .       -       0       Parent=Transcript:D1007.5b.2</span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">I   Coding_transcript       exon    4583426 4583509 .       -       0       Parent=Transcript:D1007.5b.2</span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">I   Coding_transcript       exon    4583560 4583805 .       -       0       Parent=Transcript:D1007.5b.2</span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">I   Coding_transcript       gene    4580693 4583815 .       -       .       ID=Gene:WBGene00017003</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

149

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

153

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

154

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<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>

</pre>

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</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

157

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

159

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">I   Coding_transcript       exon    4580993 4581241 .       -       0       Parent=Transcript:D1007.5a</span>

</pre>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">I   Coding_transcript       exon    4581664 4582026 .       -       0       Parent=Transcript:D1007.5a</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">I   Coding_transcript       exon    4582412 4582718 .       -       1       Parent=Transcript:D1007.5a</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">I   Coding_transcript       exon    4583190 4583374 .       -       0       Parent=Transcript:D1007.5a</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">I   Coding_transcript       exon    4583426 4583509 .       -       0       Parent=Transcript:D1007.5a</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">I   Coding_transcript       exon    4583560 4583805 .       -       0       Parent=Transcript:D1007.5a</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">I   Coding_transcript       five_prime_UTR  4583806 4583811 .       -       .       Parent=Transcript:D1007.5a</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">I   Coding_transcript       three_prime_UTR 4580693 4580992 .       -       .       Parent=Transcript:D1007.5a</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">I   Coding_transcript       intron  4582027 4582411 .       -       .       Parent=Transcript:D1007.5a;confirmed_est=EB994038</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">I   Coding_transcript       intron  4581242 4581663 .       -       .       Parent=Transcript:D1007.5a;confirmed_est=EB994038,OSTR085G5_1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">I   Coding_transcript       intron  4583375 4583425 .       -       .       Parent=Transcript:D1007.5a;confirmed_est=EC038345,OSTF085G5_1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">I   Coding_transcript       intron  4583510 4583559 .       -       .       Parent=Transcript:D1007.5a;confirmed_est=EC038345,OSTF085G5_1</span>

</pre>

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<pre style="margin: 0;">+<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>

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</table>

<br>

</li>

<li id="39e312c030efe5a4955659d6cce831c39973fe1f">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#39e312c030efe5a4955659d6cce831c39973fe1f"><strong>Tests/GFF/ensembl_gtf.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<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="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<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>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<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>

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</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<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>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<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>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<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>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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 new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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 new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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 new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

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<br>

</li>

<li id="baeab9a85d51d35425482edf0e78b2c50bea1824">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#baeab9a85d51d35425482edf0e78b2c50bea1824"><strong>Tests/GFF/glimmer_nokeyval.gff3</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##sequence-region scaffold4215_3 1 6526</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">scaffold4215_3        glimmer gene    3       62      .       -       .       ID=GL0000006;Name=GL0000006;Lack 3'-end;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">scaffold4215_3        glimmer mRNA    3       62      .       -       .       ID=GL0000006;Name=GL0000006;Parent=GL0000006;Lack 3'-end;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">scaffold4215_3        glimmer CDS     3       62      2.84    -       0       Parent=GL0000006;Lack 3'-end;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">scaffold4215_3        glimmer gene    124     1983    .       -       .       ID=GL0000007;Name=GL0000007;Complete;</span></pre>

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</table>

<br>

</li>

<li id="e433c519d4214d8282d31ee25c725c2fe46dfd9b">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#e433c519d4214d8282d31ee25c725c2fe46dfd9b"><strong>Tests/GFF/hybrid1.gff3</strong></a>

<hr>

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##sequence-region foo 1 100</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##feature-ontology bar</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##attribute-ontology baz</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##source-ontology boo</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##sequence-region chr17 62467934 62469545 </span>

</pre>

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7

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">chr17 UCSC    CDS     62468039        62468236        .       -       1       Parent=A00469</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">chr17 UCSC    CDS     62468490        62468654        .       -       2       Parent=A00469</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">chr17        UCSC    CDS     62468747        62468866        .       -       1       Parent=A00469</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">chr17        UCSC    CDS     62469076        62469236        .       -       1       Parent=A00469</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">chr17        UCSC    CDS     62469497        62469506        .       -       0       Parent=A00469</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">###</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">##FASTA</span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">>chr17</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">GATTACA</span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">GATTACA</span></pre>

</td>

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</table>

<br>

</li>

<li id="595e6a53853ddb03fefccd0c05a294b9ed7d2d83">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#595e6a53853ddb03fefccd0c05a294b9ed7d2d83"><strong>Tests/GFF/jgi_gff2.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chr_1 JGI     exon    37061   37174   .       -       .       name "fgenesh1_pg.C_chr_1000007"; transcriptId 873</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">chr_1 JGI     exon    37315   37620   .       -       .       name "fgenesh1_pg.C_chr_1000007"; transcriptId 873</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<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>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">chr_1 JGI     exon    37752   38216   .       -       .       name "fgenesh1_pg.C_chr_1000007"; transcriptId 873</span>

</pre>

</td>

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6

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<pre style="margin: 0;">+<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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</table>

<br>

</li>

<li id="69ca99a2972dee23c74045eb96a2fd7f9959cf55">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#69ca99a2972dee23c74045eb96a2fd7f9959cf55"><strong>Tests/GFF/mouse_extra_comma.gff3</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chr17 RefSeq  gene    6797760 6818159 .       +       .       ID=NC_000083.5:LOC100040603;Name=NC_000083.5:LOC100040603</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">chr17 RefSeq  mRNA    6797760 6818159 .       +       .       ID=XM_001475631.1;Parent=NC_000083.5:LOC100040603</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">chr17 RefSeq  protein 6806527 6812289 .       +       .       ID=;Parent=XM_001475631.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">chr17 RefSeq  five_prime_UTR  6797760 6797769 .       +       .       Parent=XM_001475631.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">chr17 RefSeq  five_prime_UTR  6806513 6806526 .       +       .       Parent=XM_001475631.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">chr17 RefSeq  CDS     6806527 6806553 .       +       0       Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">chr17 RefSeq  CDS     6808204 6808245 .       +       0       Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">chr17 RefSeq  CDS     6811330 6811453 .       +       0       Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">chr17 RefSeq  CDS     6811792 6811869 .       +       2       Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">chr17        RefSeq  CDS     6812219 6812289 .       +       2       Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">chr17        RefSeq  three_prime_UTR 6812290 6818159 .       +       .       Parent=XM_001475631.1</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">chr17        RefSeq  exon    6797760 6797769 .       +       .       Parent=XM_001475631.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">chr17        RefSeq  exon    6806513 6806553 .       +       .       Parent=XM_001475631.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">chr17        RefSeq  exon    6808204 6808245 .       +       .       Parent=XM_001475631.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">chr17        RefSeq  exon    6811330 6811453 .       +       .       Parent=XM_001475631.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">chr17        RefSeq  exon    6811792 6811869 .       +       .       Parent=XM_001475631.1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">chr17        RefSeq  exon    6812219 6818159 .       +       .       Parent=XM_001475631.1</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="284adb09db73557c24d311d7a9916b60e0a5a809">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#284adb09db73557c24d311d7a9916b60e0a5a809"><strong>Tests/GFF/ncbi_gff3.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##source-version NCBI C++ formatter 0.2</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##date 2009-04-25</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##Type DNA NC_008596.1</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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21

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<pre style="margin: 0;">+<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>

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</table>

<br>

</li>

<li id="29db11f1f11aaaca59fe32a3ff3453b37254497b">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#29db11f1f11aaaca59fe32a3ff3453b37254497b"><strong>Tests/GFF/problem_sequence_region.gff3</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#!gff-spec-version 1.21</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">#!processor NCBI annotwriter</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##sequence-region  1 2482535</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1282</span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

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</li>

<li id="b9e1aa3c398e2345520376b31a5cb2096bef8dba">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#b9e1aa3c398e2345520376b31a5cb2096bef8dba"><strong>Tests/GFF/spaces.gff3</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">contig1       .       gene    1544    2057    .       -       .       ID=contig1.1</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">contig1       .       mRNA    1544    2057    .       -       .       ID=mRNA.contig1.1;Parent=contig1.1   </span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">contig1       .       mRNA    1544    2057    .       -       .        foo=bar;ID=mRNA.contig1.1;Parent=contig1.1   </span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">contig1       .       mRNA    1544    2057    .       -       .       ID=mRNA.contig1.1;Parent=contig1.1; foo=bar</span></pre>

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<br>

</li>

<li id="5b5a49f848dceb982e0f0b9221513c0367d4a001">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#5b5a49f848dceb982e0f0b9221513c0367d4a001"><strong>Tests/GFF/trans_splicing.gff3</strong></a>

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1

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">1     manual  exon    9559    9672    .       +       .       Parent=mRNA43</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">1     manual  CDS     9559    9672    .       +       0       Parent=mRNA43</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">1     manual  exon    112442  112673  .       +       .       Parent=mRNA43</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">1     manual  CDS     112442  112673  .       +       0       Parent=mRNA43</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">1     manual  intron  112674  113215  .       +       .       Parent=mRNA43</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">1    manual  exon    113216  113241  .       +       .       Parent=mRNA43</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">1    manual  CDS     113216  113241  .       +       2       Parent=mRNA43</span></pre>

</td>

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<br>

</li>

<li id="6c671f0bd5a210f7a94e0c4bab6fd5c1e6068025">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#6c671f0bd5a210f7a94e0c4bab6fd5c1e6068025"><strong>Tests/GFF/transcripts.gff3</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##date 2013-11-13</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">edit_test.fa  .       gene    500     2610    .       +       .       ID=newGene</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">edit_test.fa  .       five_prime_UTR  500     802     .       +       .       Parent=t1</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">edit_test.fa  .       CDS     803     1012    .       +       .       Parent=t1</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">edit_test.fa  .       three_prime_UTR 1013    1168    .       +       .       Parent=t1</span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">edit_test.fa  .       three_prime_UTR 1475    1654    .       +       .       Parent=t1</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">edit_test.fa  .       three_prime_UTR 1720    1908    .       +       .       Parent=t1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">edit_test.fa .       three_prime_UTR 2047    2385    .       +       .       Parent=t1</span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">edit_test.fa .       CDS     1050    1196    .       +       .       Parent=t2</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">edit_test.fa .       CDS     1472    1651    .       +       .       Parent=t2</span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">edit_test.fa .       CDS     1732    2610    .       +       .       Parent=t2</span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">edit_test.fa .       CDS     1050    1196    .       +       .       Parent=t3</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">edit_test.fa .       CDS     1472    1651    .       +       .       Parent=t3</span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">edit_test.fa .       CDS     1732    2610    .       +       .       Parent=t3</span></pre>

</td>

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<br>

</li>

<li id="f4023d8db326a19aa73f1e08c79ba89f9c8ec4ee">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#f4023d8db326a19aa73f1e08c79ba89f9c8ec4ee"><strong>Tests/GFF/unescaped-semicolon.gff3</strong></a>

<hr>

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>

</pre>

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<pre style="margin: 0;">+<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>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>

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</li>

<li id="dc72ce464baa5740ce7acbbe1c08bab5e1dc1039">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#dc72ce464baa5740ce7acbbe1c08bab5e1dc1039"><strong>Tests/GFF/wormbase_gff2.txt</strong></a>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">I     Coding_transcript       intron  12759829        12759948        .       -       .       Transcript "B0019.1" ; Confirmed_EST EC034652</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">I     Coding_transcript       intron  12760014        12760226        .       -       .       Transcript "B0019.1" ; Confirmed_EST EC034652</span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">I     Coding_transcript       intron  12760320        12760364        .       -       .       Transcript "B0019.1" ; Confirmed_EST yk1054h04.3</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">I     Coding_transcript       intron  12760495        12760833        .       -       .       Transcript "B0019.1" ; Confirmed_EST EC027594</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">I     Coding_transcript       intron  12760905        12761171        .       -       .       Transcript "B0019.1" ; Confirmed_EST EC027594</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">I     Coding_transcript       intron  12761517        12761798        .       -       .       Transcript "B0019.1" ; Confirmed_EST EC027594</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">I     Coding_transcript       intron  12761954        12762126        .       -       .       Transcript "B0019.1" ; Confirmed_EST yk262g9.5</span>

</pre>

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</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">I    Coding_transcript       intron  12762269        12762647        .       -       .       Transcript "B0019.1" ; Confirmed_EST yk262g9.5</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">I    Coding_transcript       intron  12762807        12763111        .       -       .       Transcript "B0019.1" ; Confirmed_EST yk1056c07.5</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">I    Coding_transcript       intron  12763250        12763447        .       -       .       Transcript "B0019.1" ; Confirmed_EST yk1056c07.5</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">I    Coding_transcript       intron  12763656        12763728        .       -       .       Transcript "B0019.1" ; Confirmed_EST yk1056c07.5</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<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>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">I    Coding_transcript       exon    12759582        12759828        .       -       .       Transcript "B0019.1"</span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">I    Coding_transcript       exon    12759949        12760013        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">I    Coding_transcript       exon    12760227        12760319        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">I    Coding_transcript       exon    12760365        12760494        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">I    Coding_transcript       exon    12760834        12760904        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">I    Coding_transcript       exon    12761172        12761516        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">I    Coding_transcript       exon    12761799        12761953        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">I    Coding_transcript       exon    12762127        12762268        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">I    Coding_transcript       exon    12762648        12762806        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">I    Coding_transcript       exon    12763112        12763249        .       -       .       Transcript "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">I    Coding_transcript       exon    12763448        12763655        .       -       .       Transcript "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">I    Coding_transcript       exon    12763729        12763882        .       -       .       Transcript "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">I    Coding_transcript       exon    12763979        12764102        .       -       .       Transcript "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">I    Coding_transcript       exon    12764291        12764471        .       -       .       Transcript "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">I    Coding_transcript       exon    12764812        12764949        .       -       .       Transcript "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">I    GenePair_STS    PCR_product     12762449        12764118        .       +       .       PCR_product "sjj_B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">I    Expr_profile    experimental_result_region      12762449        12764118        .       +       .       Expr_profile "B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">I    Allele  SNP     12764272        12764272        .       +       .       Variation "snp_B0019[1]" ; Interpolated_map_position "14.003" ; ; RFLP "No"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">I    Promoterome     PCR_product     12764938        12766937        .       +       .       PCR_product "p_B0019.1_93"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">I    Oligo_set       reagent 12759745        12761589        .       -       .       Oligo_set "Aff_B0019.1"</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">I    Orfeome PCR_product     12759747        12764936        .       -       .       PCR_product "mv_B0019.1" ; Amplified 1 ; Amplified 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">I    Coding_transcript       three_prime_UTR 12759582        12759744        .       -       .       Transcript "B0019.1"</span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">I    Coding_transcript       coding_exon     12759949        12760013        .       -       2       Transcript "B0019.1" ; CDS "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">I    Coding_transcript       coding_exon     12760227        12760319        .       -       2       Transcript "B0019.1" ; CDS "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">I    Coding_transcript       coding_exon     12760365        12760494        .       -       0       Transcript "B0019.1" ; CDS "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">I    Coding_transcript       five_prime_UTR  12764938        12764949        .       -       .       Transcript "B0019.1"</span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">X    gene    processed_transcript    944828  948883  .       -       .       Gene "WBGene00004893"</span></pre>

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<br>

</li>

<li id="90597a4495f86cc9aa824359f59cbfc74bba4474">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#90597a4495f86cc9aa824359f59cbfc74bba4474"><strong>Tests/GFF/wormbase_gff2_alt.txt</strong></a>

<hr>

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Remanei_genome        Genomic_canonical       region  1       7816    .       +       .       Sequence "Contig1020";</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Contig102     WU_MERGED       CDS     1629    3377    .       -       .       CDS "cr01.sctg102.wum.2.1"</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Contig102     WU_MERGED       coding_exon     2927    3377    .       -       .       CDS "cr01.sctg102.wum.2.1"</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Contig102     WU_MERGED       coding_exon     2474    2875    .       -       .       CDS "cr01.sctg102.wum.2.1"</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Contig102     WU_MERGED       coding_exon     1928    2430    .       -       .       CDS "cr01.sctg102.wum.2.1"</span>

</pre>

</td>

</tr>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Contig102     WU_MERGED       coding_exon     1629    1883    .       -       .       CDS "cr01.sctg102.wum.2.1"</span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Contig102     WU_MERGED       intron  2876    2926    .       -       .       CDS "cr01.sctg102.wum.2.1"</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Contig102     WU_MERGED       intron  2431    2473    .       -       .       CDS "cr01.sctg102.wum.2.1"</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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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</table>

<br>

</li>

<li id="936fbcee4a35275ed493abce9f6c9e7f4180931b">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#936fbcee4a35275ed493abce9f6c9e7f4180931b"><strong>Tests/test_GFFSeqIOFeatureAdder.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pprint</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">six</span></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">six</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">BCBio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GFF</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Seq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Seq</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">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="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>

</pre>

</td>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">        <span class="s" style="color: #d14;">"""General map reduce framework without parallelization.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">        <span class="s" style="color: #d14;">"""Map reduce framework parallelized using disco.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">            <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">disco</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">            <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">            <span class="k" style="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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;">+<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="n" style="color: #333;">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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_disco_host</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># second gene feature is multi-parent</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">    <span class="s" style="color: #d14;">"""Real live GFF3 tests from WormBase and NCBI.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;">    Uses GFF3 data from:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;">    ftp://ftp.wormbase.org/pub/wormbase/genomes/c_elegans/</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;">    genome_feature_tables/GFF3/</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>

</pre>

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67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;">    and from NCBI.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">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="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">        <span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">                <span class="s" style="color: #d14;">"data_files_WS198"</span></span>

</pre>

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77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">        <span class="s" style="color: #d14;">"""Test the full C elegans chromosome and GFF files.</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"></span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;">        to run this.</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python">        <span class="n" style="color: #333;">seq_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python">            <span class="k" style="font-weight: 600;">pass</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python">        <span class="s" style="color: #d14;">"""Internal reusable function to get the sequence dictionary.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_seq_file</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">        <span class="n" style="color: #333;">seq_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">        <span class="s" style="color: #d14;">"""Calculate possible queries to limit a GFF file.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFExaminer</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">available_limits</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python">        <span class="n" style="color: #333;">pprint</span><span class="p">.</span><span class="n" style="color: #333;">pprint</span><span class="p">(</span><span class="n" style="color: #333;">possible_limits</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python">        <span class="s" style="color: #d14;">"""Summarize parent-child relationships in a GFF file.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFExaminer</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">parent_child_map</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python">        <span class="n" style="color: #333;">pprint</span><span class="p">.</span><span class="n" style="color: #333;">pprint</span><span class="p">(</span><span class="n" style="color: #333;">pc_map</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python">        <span class="s" style="color: #d14;">"""Summarize parent-child relationships in a GFF file.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFExaminer</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">parent_child_map</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

136

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<pre style="margin: 0;">+<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="n" style="color: #333;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python">                    <span class="n" style="color: #333;">gff_examiner</span><span class="p">.</span><span class="n" style="color: #333;">parent_child_map</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python">                    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

148

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_seq_dict</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_seq_dict</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># first gene feature is plain</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># 15 final CDS regions</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python">        <span class="s" style="color: #d14;">"""Verify correct nesting of features with multiple parents.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_seq_dict</span><span class="p">()</span></span>

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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python">        <span class="p">)</span></span>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># second gene feature is multi-parent</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;">+<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="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># no error -- problem</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">(</span><span class="s" style="color: #d14;">'Did not complain with missing dictionary'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python">            <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python">        <span class="s" style="color: #d14;">"""Prepare unknown base sequences with the correct length.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python">        <span class="s" style="color: #d14;">"""Check GFF annotations placed on an entire sequence.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_ann_file</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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="n" style="color: #333;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python">        <span class="s" style="color: #d14;">"""Iterated parsing in GFF3 files with nested features.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse_in_parts</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python">        <span class="s" style="color: #d14;">"""Iterated interface using a limit query on GFF3 files.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_ncbi</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_ncbi</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse_simple</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse_simple</span><span class="p">(</span><span class="n" style="color: #333;">test_gff</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python">        <span class="s" style="color: #d14;">"""Correctly handle GFF3 files with extra trailing commas.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tfile</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python">            <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python">        <span class="n" style="color: #333;">in_handle</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python">                    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"></span>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python">        <span class="s" style="color: #d14;">"""Handle GFF3 files with keys and no values.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">tfile</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python">        <span class="s" style="color: #d14;">"""Fix keys with problematic whitespace.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse_simple</span><span class="p">(</span><span class="n" style="color: #333;">tfile</span><span class="p">)):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">in_handle</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python">    <span class="s" style="color: #d14;">"""Test reading output from SOLiD analysis, as GFF3.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;">    See more details on SOLiD GFF here:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;">    http://solidsoftwaretools.com/gf/project/matogff/</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python">        <span class="s" style="color: #d14;">"""Basic parsing of SOLiD GFF results files.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">))</span></span>

</pre>

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364

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

374

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

375

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

376

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python">        <span class="s" style="color: #d14;">"""Iterated parsing in a flat file without nested features.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

377

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

378

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<pre style="margin: 0;">+<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="n" style="color: #333;">GFFParser</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

379

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse_in_parts</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python">            <span class="n" style="color: #333;">feature_sizes</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

382

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

384

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

386

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC386" class="line" lang="python">        <span class="s" style="color: #d14;">"""Adjust lines during parsing to fix potential GFF problems.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

387

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

389

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

390

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

391

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

392

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

393

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

394

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

395

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

396

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<pre style="margin: 0;">+<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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

397

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">)]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

399

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

400

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

402

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python">    <span class="s" style="color: #d14;">"""Parse GFF2 and GTF files, building features.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python">        <span class="s" style="color: #d14;">"""Parse out basic attributes of GFF2 from Ensembl GTF.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">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="n" style="color: #333;">keys</span><span class="p">())</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python">        <span class="n" style="color: #333;">qual_keys</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python">        <span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python">        <span class="s" style="color: #d14;">"""Parsing of tricky semi-colon positions in WormBase GFF2.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"></span>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<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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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"><span class="s" style="color: #d14;">        the combined feature will not be maintained.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'osFTL6'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'protein, expressed'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_jgi_file</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"><span class="s" style="color: #d14;">        XXX sub_features no longer supported in Biopython</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ensembl_file</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"></span>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

491

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

493

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

494

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wb_alt_file</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

496

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

497

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<pre style="margin: 0;">+<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="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">rec_dict</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

500

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

503

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python">        <span class="s" style="color: #d14;">"""Test iterated features with GFF2 files, breaking without parents.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

505

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

506

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<pre style="margin: 0;">+<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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

507

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<pre style="margin: 0;">+<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="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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508

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python">            <span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

509

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

510

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

511

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<pre style="margin: 0;">+<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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

512

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

513

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

514

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

515

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<pre style="margin: 0;">+<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>

</pre>

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python">    <span class="s" style="color: #d14;">"""Tests for parsing directives and other meta-data.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

521

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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

522

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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC524" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python">        <span class="s" style="color: #d14;">"""Parse out top level meta-data supplied in a GFF3 file.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC527" 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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC528" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC529" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC530" 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>

</pre>

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<pre style="margin: 0;">+<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;">'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>

</pre>

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<pre style="margin: 0;">+<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;">'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>

</pre>

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<pre style="margin: 0;">+<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;">'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>

</pre>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC535" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python">        <span class="s" style="color: #d14;">"""Parse FASTA sequence information contained in a GFF3 file.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC538" 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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

540

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<pre style="margin: 0;">+<span id="LC540" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

541

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<pre style="margin: 0;">+<span id="LC541" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

542

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

543

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<pre style="margin: 0;">+<span id="LC543" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

544

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python">        <span class="s" style="color: #d14;">"""Perform high level examination of files with FASTA directives.</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

546

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python">        <span class="n" style="color: #333;">examiner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GFFExaminer</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

547

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<pre style="margin: 0;">+<span id="LC547" 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="n" style="color: #333;">parent_child_map</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

548

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<pre style="margin: 0;">+<span id="LC548" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

549

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<pre style="margin: 0;">+<span id="LC549" 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="n" style="color: #333;">available_limits</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff_file</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

550

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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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="n" style="color: #333;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> \</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

552

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<pre style="margin: 0;">+<span id="LC552" 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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

553

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC554" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

555

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python">        <span class="s" style="color: #d14;">"""Avoid issues with sequence region directives lacking contigs</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

556

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

557

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<pre style="margin: 0;">+<span id="LC557" 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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_problem_seq_region_file</span><span class="p">))</span></span>

</pre>

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558

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<pre style="margin: 0;">+<span id="LC558" 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>

</pre>

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559

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<pre style="margin: 0;">+<span id="LC559" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

560

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<pre style="margin: 0;">+<span id="LC560" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

561

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

562

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

563

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<pre style="margin: 0;">+<span id="LC563" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

564

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python">    <span class="s" style="color: #d14;">"""Tests to write SeqFeatures to GFF3 output format.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

565

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

566

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC567" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

568

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">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="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

570

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC570" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

571

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC571" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

572

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC572" class="line" lang="python">        <span class="bp" style="color: #999;">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="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

573

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"></span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

574

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<pre style="margin: 0;">+<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_gff3_to_gff3</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

575

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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python">        <span class="s" style="color: #d14;">"""Read in and write out GFF3 without any loss of information.</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

576

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

577

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<pre style="margin: 0;">+<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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_test_gff_file</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python">        <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python">        <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python">        <span class="n" style="color: #333;">wrote_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">())</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

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<pre style="margin: 0;">+<span id="LC581" 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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">wrote_handle</span><span class="p">))</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

582

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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

583

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python">        <span class="n" style="color: #333;">orig_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

584

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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python">        <span class="n" style="color: #333;">re_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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="nb" style="color: #0086b3;">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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

586

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<pre style="margin: 0;">+<span id="LC586" 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="nb" style="color: #0086b3;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

587

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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python">            <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">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="nb" style="color: #0086b3;">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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

588

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

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<pre style="margin: 0;">+<span id="LC589" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python">        <span class="s" style="color: #d14;">"""Read in GFF2 and write out as GFF3.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

591

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

592

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<pre style="margin: 0;">+<span id="LC592" 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="n" style="color: #333;">to_dict</span><span class="p">(</span><span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_wormbase_file</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python">        <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

594

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python">        <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">out_handle</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

595

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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python">        <span class="n" style="color: #333;">wrote_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">out_handle</span><span class="p">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">())</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

596

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># check some tricky lines in the GFF2 file</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

597

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<pre style="margin: 0;">+<span id="LC597" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

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<pre style="margin: 0;">+<span id="LC598" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

599

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<pre style="margin: 0;">+<span id="LC599" 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="n" style="color: #333;">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>

</pre>

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600

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<pre style="margin: 0;">+<span id="LC600" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

601

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<pre style="margin: 0;">+<span id="LC601" 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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

602

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<pre style="margin: 0;">+<span id="LC602" 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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

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<pre style="margin: 0;">+<span id="LC603" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

604

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<pre style="margin: 0;">+<span id="LC604" 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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

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<pre style="margin: 0;">+<span id="LC605" 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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

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<pre style="margin: 0;">+<span id="LC606" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<pre style="margin: 0;">+<span id="LC607" 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="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

608

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<pre style="margin: 0;">+<span id="LC608" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC610" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python">        <span class="s" style="color: #d14;">"""Write out GFF3 from SeqRecord inputs.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python">        <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="s" style="color: #d14;">"GATCGATCGATCGATCGATC"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC614" 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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC615" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC616" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python">        <span class="n" style="color: #333;">top_feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqFeature</span><span class="p">(</span><span class="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

618

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<pre style="margin: 0;">+<span id="LC618" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python">            <span class="n" style="color: #333;">SeqFeature</span><span class="p">(</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python">            <span class="n" style="color: #333;">SeqFeature</span><span class="p">(</span><span class="n" style="color: #333;">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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python">        <span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC622" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

623

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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python">        <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

624

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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python">        <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

625

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<pre style="margin: 0;">+<span id="LC625" 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="n" style="color: #333;">getvalue</span><span class="p">().</span><span class="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

626

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<pre style="margin: 0;">+<span id="LC626" 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

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<pre style="margin: 0;">+<span id="LC627" 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

628

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python">        <span class="k" style="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="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

629

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<pre style="margin: 0;">+<span id="LC629" 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="n" style="color: #333;">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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

630

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<pre style="margin: 0;">+<span id="LC630" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

631

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC631" class="line" lang="python">        <span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

632

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<pre style="margin: 0;">+<span id="LC632" 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="n" style="color: #333;">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>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

633

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

634

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<pre style="margin: 0;">+<span id="LC634" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python">        <span class="s" style="color: #d14;">"""Include FASTA records in GFF output.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="python">        <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="s" style="color: #d14;">"GATCGATCGATCGATCGATC"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

638

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<pre style="margin: 0;">+<span id="LC638" 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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC639" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC640" 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;">SeqFeature</span><span class="p">(</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC641" class="line" lang="python">        <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC642" class="line" lang="python">        <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC643" 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="n" style="color: #333;">getvalue</span><span class="p">().</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC644" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC645" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC646" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC647" 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="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC649" 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="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<td class="new_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC650" class="line" lang="python">        <span class="s" style="color: #d14;">"""Write single SeqRecords.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC651" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python">        <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Seq</span><span class="p">(</span><span class="s" style="color: #d14;">"GATCGATCGATCGATCGATC"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC653" 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;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC654" 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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<pre style="margin: 0;">+<span id="LC655" 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;">SeqFeature</span><span class="p">(</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="python">        <span class="n" style="color: #333;">out_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python">        <span class="n" style="color: #333;">GFF</span><span class="p">.</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC658" 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="n" style="color: #333;">getvalue</span><span class="p">().</span><span class="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC659" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC660" 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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC663" 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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<pre style="margin: 0;">+<span id="LC664" 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;">testing_suite</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC665" 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="n" style="color: #333;">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>

</pre>

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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python">    <span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">test_suite</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"></span>

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<pre style="margin: 0;">+<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;">testing_suite</span><span class="p">():</span></span>

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python">    <span class="s" style="color: #d14;">"""Generate the suite of tests.</span></span>

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">+<span id="LC672" 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="n" style="color: #333;">TestSuite</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC673" 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="n" style="color: #333;">TestLoader</span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC674" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC675" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#tests = [GFF3Test]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC677" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC678" 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="n" style="color: #333;">loadTestsFromTestCase</span><span class="p">(</span><span class="n" style="color: #333;">test</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python">        <span class="n" style="color: #333;">test_suite</span><span class="p">.</span><span class="n" style="color: #333;">addTest</span><span class="p">(</span><span class="n" style="color: #333;">cur_suite</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_suite</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC681" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC683" 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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">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>

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<br>

</li>

<li id="788d776bfe907f02f738f7115e219184170cb4f7">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#788d776bfe907f02f738f7115e219184170cb4f7"><strong>bcbio_gff.egg-info/PKG-INFO</strong></a>

<hr>

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1

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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.0</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(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: bcbio-gff</span>

</pre>

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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(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.6.<span class="idiff left right">6</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.6.<span class="idiff left right">7</span></span>

</pre>

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4

</td>

<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Read and write Generic Feature Format (GFF) with Biopython integration.</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/chapmanb/bcbb/tree/master/gff</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Brad Chapman</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Author-email: chapmanb@50mail.com</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="new_line diff-line-num old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">UNKNOWN</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">Biopython License</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Description: UNKNOWN</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Platform: UNKNOWN</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="944df03d39008ed8c63cac4c573db3e9218908ca">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#944df03d39008ed8c63cac4c573db3e9218908ca"><strong>bcbio_gff.egg-info/SOURCES.txt</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,6 +8,29 @@ BCBio/GFF/GFFOutput.py</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">BCBio/GFF/GFFParser.py</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">BCBio/GFF/__init__.py</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">BCBio/GFF/_utils.py</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Scripts/gff/access_gff_index.py</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Scripts/gff/genbank_to_gff.py</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Scripts/gff/gff2_to_gff3.py</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Scripts/gff/gff_to_biosql.py</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Scripts/gff/gff_to_genbank.py</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Tests/test_GFFSeqIOFeatureAdder.py</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Tests/GFF/F3-unique-3.v2.gff</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Tests/GFF/c_elegans_WS199_ann_gff.txt</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Tests/GFF/c_elegans_WS199_dna_shortened.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Tests/GFF/c_elegans_WS199_shortened_gff.txt</span>

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Tests/GFF/ensembl_gtf.txt</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Tests/GFF/glimmer_nokeyval.gff3</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Tests/GFF/hybrid1.gff3</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Tests/GFF/jgi_gff2.txt</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Tests/GFF/mouse_extra_comma.gff3</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Tests/GFF/ncbi_gff3.txt</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Tests/GFF/problem_sequence_region.gff3</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Tests/GFF/spaces.gff3</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Tests/GFF/trans_splicing.gff3</span>

</pre>

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30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Tests/GFF/transcripts.gff3</span>

</pre>

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31

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Tests/GFF/unescaped-semicolon.gff3</span>

</pre>

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32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Tests/GFF/wormbase_gff2.txt</span>

</pre>

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33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Tests/GFF/wormbase_gff2_alt.txt</span>

</pre>

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11

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34

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">bcbio_gff.egg-info/PKG-INFO</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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35

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">bcbio_gff.egg-info/SOURCES.txt</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">bcbio_gff.egg-info/dependency_links.txt</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="de6397a38781ddc950257fbb3e3ff8f75e8ba390">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#de6397a38781ddc950257fbb3e3ff8f75e8ba390"><strong>bcbio_gff.egg-info/requires.txt</strong></a>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">six</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">biopython</span></pre>

</td>

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</table>

<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/0195e22774cb530a026fc57fdfe9096c350997d6#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,8 +14,9 @@ setup(name="bcbio-gff",</td>

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14

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14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">      <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span></span>

</pre>

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15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">      <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Brad Chapman"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">      <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"chapmanb@50mail.com"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">      <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Biopython License"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="new_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">      <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Read and write Generic Feature Format (GFF) with Biopython integration."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">      <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://github.com/chapmanb/bcbb/tree/master/gff"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">      <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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<td class="new_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python">      <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"six"</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">      <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"six"</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"biopython"</span></span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python">      <span class="p">)</span></span></pre>

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