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<h3>
Nilesh Patra pushed to branch master
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/858f20e31b2737cf6ac2f7664cede24f652b7eaa">858f20e3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-10T00:27:03+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.6.8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/18ee330cefedcb1e25f653dd72a6bfd41ef8ff0c">18ee330c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-10T00:27:04+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.6.8'
Update to upstream version '0.6.8'
with Debian dir fcd1e1735185d0fdbd55698c219f4309a57cf92b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/commit/a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8">a0c8f7c5</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-11-10T00:27:39+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ba3404825a4d349f45211497986428bd4b75a757">
BCBio/GFF/GFFParser.py
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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="#2598951dd9ce972e3fb974dd1069ecb0ac43f16b">
<span class="new-file">
+
Tests/GFF/hybrid2.fa
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<a href="#162c3679ebe63ccaacf9c1837a27f907a63c61a3">
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+
Tests/GFF/hybrid2.gff3
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<li class="file-stats">
<a href="#936fbcee4a35275ed493abce9f6c9e7f4180931b">
Tests/test_GFFSeqIOFeatureAdder.py
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<li class="file-stats">
<a href="#788d776bfe907f02f738f7115e219184170cb4f7">
bcbio_gff.egg-info/PKG-INFO
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<li class="file-stats">
<a href="#944df03d39008ed8c63cac4c573db3e9218908ca">
bcbio_gff.egg-info/SOURCES.txt
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</ul>
<h4>Changes:</h4>
<li id="ba3404825a4d349f45211497986428bd4b75a757">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#ba3404825a4d349f45211497986428bd4b75a757"><strong>BCBio/GFF/GFFParser.py</strong></a>
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<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">@@ -36,10 +36,8 @@ from Bio.SeqRecord import SeqRecord</td>
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<td class="old_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">
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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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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(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="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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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(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="38" style="width: 35px; color: rgba(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="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>
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<td class="old_line diff-line-num old" data-linenumber="39" 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="39" 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="LC39" class="line" lang="python"></span>
</pre>
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<td class="old_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="LC39" 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="LC40" 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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<td class="old_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(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="LC41" 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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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(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="LC42" 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>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="48" style="width: 35px; color: rgba(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">@@ -50,7 +48,6 @@ def _gff_line_map(line, params):</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> - determines the type of attribute (flat, parent, child or annotation)</span></span>
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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(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="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> - generates a dictionary of GFF info which can be serialized as JSON</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" 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>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"""Merge key-values escaped by quotes that are improperly split at semicolons.</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="64" style="width: 35px; color: rgba(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">@@ -67,7 +64,6 @@ def _gff_line_map(line, params):</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC66" 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="LC67" 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="LC68" 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="LC69" class="line" lang="python"></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">@@ -157,14 +153,15 @@ def _gff_line_map(line, params):</td>
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<pre style="margin: 0;"> <span id="LC153" 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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154
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<pre style="margin: 0;"> <span id="LC154" 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="LC155" 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="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>
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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="LC156" 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="LC157" 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="LC158" class="line" lang="python"> <span class="s" style="color: #d14;">"start_codon"</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC159" 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>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC162" 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="LC163" class="line" lang="python"></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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164
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<pre style="margin: 0;">+<span id="LC164" 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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168
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165
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<pre style="margin: 0;"> <span id="LC165" 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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169
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166
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<pre style="margin: 0;"> <span id="LC166" 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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170
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167
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<pre style="margin: 0;"> <span id="LC167" 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="diff-line-num unfold js-unfold old_line" data-linenumber="173" style="width: 35px; color: rgba(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="170" style="width: 35px; color: rgba(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">@@ -173,7 +170,8 @@ def _gff_line_map(line, params):</td>
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173
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170
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<pre style="margin: 0;"> <span id="LC170" 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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174
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171
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<pre style="margin: 0;"> <span id="LC171" 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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175
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172
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<pre style="margin: 0;"> <span id="LC172" 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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176
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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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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">cur_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="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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174
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<pre style="margin: 0;">+<span id="LC174" 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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177
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175
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<pre style="margin: 0;"> <span id="LC175" 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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178
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176
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<pre style="margin: 0;"> <span id="LC176" 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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179
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" style="width: 35px; color: rgba(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">@@ -204,7 +202,8 @@ def _gff_line_map(line, params):</td>
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204
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202
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<pre style="margin: 0;"> <span id="LC202" 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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205
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203
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<pre style="margin: 0;"> <span id="LC203" 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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206
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204
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<pre style="margin: 0;"> <span id="LC204" 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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207
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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="LC205" 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="LC206" 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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207
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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;">'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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208
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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;">'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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209
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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;">'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 new_line" data-linenumber="234" style="width: 35px; color: rgba(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">@@ -235,7 +234,6 @@ def _gff_line_map(line, params):</td>
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<pre style="margin: 0;"> <span id="LC234" 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="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC236" 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="LC237" 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="LC238" 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="LC239" 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">@@ -252,7 +250,6 @@ def _gff_line_reduce(map_results, out, params):</td>
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252
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<pre style="margin: 0;"> <span id="LC250" 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="LC251" 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="LC252" 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="LC253" 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="LC254" 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="LC255" class="line" lang="python"></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">@@ -260,7 +257,6 @@ class _MultiIDRemapper:</td>
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<pre style="margin: 0;"> <span id="LC257" 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="LC258" class="line" lang="python"><span class="s" style="color: #d14;"> parent.</span></span>
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<pre style="margin: 0;"> <span id="LC259" 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="LC260" 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="LC261" 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="LC262" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -277,11 +273,9 @@ class _MultiIDRemapper:</td>
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<pre style="margin: 0;"> <span id="LC273" 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="LC274" 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="LC275" 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="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="LC276" 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="LC277" 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="LC278" 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="LC279" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC280" 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="LC281" 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">@@ -291,7 +285,6 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC285" 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="LC286" class="line" lang="python"><span class="s" style="color: #d14;"> information.</span></span>
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<pre style="margin: 0;"> <span id="LC287" 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="LC288" 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="LC289" 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="LC290" class="line" lang="python"></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">@@ -320,7 +313,8 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC313" 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="LC314" 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="LC315" class="line" lang="python"></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="LC316" 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="LC317" 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="LC318" 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="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC320" 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="diff-line-num unfold js-unfold new_line" data-linenumber="365" style="width: 35px; color: rgba(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">@@ -371,7 +365,8 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC365" 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="LC366" 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="LC367" 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="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="LC368" 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="LC369" 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="LC370" 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="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_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>
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<pre style="margin: 0;"> <span id="LC372" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -402,12 +397,35 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_add_ann_to_rec</span><span class="p">(</span><span class="n" style="color: #333;">rec</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="LC398" 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="LC399" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_matching_record_id</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;">find_id</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="s" style="color: #d14;">"""Find a matching base record with the test identifier, handling tricky cases.</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"><span class="s" style="color: #d14;"> NCBI IDs https://en.wikipedia.org/wiki/FASTA_format#NCBI_identifiers</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Straight matches for identifiers</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">find_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">base</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">find_id</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># NCBI style IDs in find_id</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">find_id</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>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">test_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</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;">find_id</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;">1</span><span class="p">:]]:</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test_id</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">test_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">base</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test_id</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># NCBI style IDs in base IDs</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">base_id</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;">keys</span><span class="p">():</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">base_id</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>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">test_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</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;">base_id</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;">1</span><span class="p">:]]:</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">test_id</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">test_id</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">find_id</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">base_id</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_seqs</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;">recs</span><span class="p">):</span></span>
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406
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="s" style="color: #d14;">"""Add sequence information contained in the GFF3 to records.</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC425" 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;">recs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">base</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">base</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;">seq</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;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">match_id</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_matching_record_id</span><span class="p">(</span><span class="n" style="color: #333;">base</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>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match_id</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">match_id</span><span class="p">].</span><span class="n" style="color: #333;">seq</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;">seq</span></span>
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<pre style="margin: 0;"> <span id="LC429" 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="LC430" class="line" lang="python"> <span class="n" style="color: #333;">base</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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span></span>
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<pre style="margin: 0;"> <span id="LC431" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -424,15 +442,18 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC442" 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="LC443" 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="LC444" 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="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="LC445" 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="LC446" 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="LC447" 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="LC448" 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="LC449" 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="LC450" 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="LC451" 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="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="LC452" 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="LC453" 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="LC454" 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="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="LC455" 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="LC456" 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="LC457" 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="LC458" 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="LC459" 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">@@ -440,12 +461,15 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC461" 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="LC462" 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="LC463" 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="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="LC464" 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="LC465" 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="LC466" 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="LC467" 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="LC468" 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="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="LC469" 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="LC470" 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="LC471" 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="LC472" 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="LC473" 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="LC474" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC475" 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">@@ -458,7 +482,8 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC482" 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="LC483" 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="LC484" 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="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="LC485" 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="LC486" 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="LC487" 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="LC488" 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="LC489" 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">@@ -507,19 +532,20 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="s" style="color: #d14;">"""Retrieve a record to add features to.</span></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">max_loc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_dict</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">'location'</span><span class="p">,</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="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">cur_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">]]</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="n" style="color: #333;">match_id</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_matching_record_id</span><span class="p">(</span><span class="n" style="color: #333;">base</span><span class="p">,</span> <span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match_id</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">cur_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span><span class="p">[</span><span class="n" style="color: #333;">match_id</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># update generated unknown sequences with the expected maximum length</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">UnknownSeq</span><span class="p">):</span></span>
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514
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"> <span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="n" style="color: #333;">max_loc</span><span class="p">,</span> <span class="n" style="color: #333;">cur_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">_length</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_rec</span><span class="p">,</span> <span class="n" style="color: #333;">base</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="k" style="font-weight: 600;">e<span class="idiff left">xcept</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">KeyError</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_create_missing</span></span><span class="p"><span class="idiff right">:</span></span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">new_rec</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">SeqRecord</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">UnknownSeq</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">max_loc</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">]<span class="idiff right">)</span></span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">base</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">info_dict</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'rec_id'</span></span><span class="p"><span class="idiff">]]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">new_rec</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_rec</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ba</span>se</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="p"><span class="idiff right">:</span></span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left right">raise</span></span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"> <span class="k" style="font-weight: 600;">e<span class="idiff left">lif</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_create_missing</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">new_rec</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">SeqRecord</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">UnknownSeq</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">max_loc</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_dict</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'rec_id'</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">base</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;">info_dict</span><span class="p">[</span><span class="s" style="color: #d14;">'rec_id'</span><span class="p">]<span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">new_rec</span></span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span> <span class="n" style="color: #333;">new_rec</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">base</span></span></span>
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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">
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">el</span>se</span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">raise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">KeyError</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Did not find matching record in %s for %s"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">base</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info_dict</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_missing_parent</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;">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="LC551" class="line" lang="python"> <span class="s" style="color: #d14;">"""Add a new feature that is missing from the GFF file.</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">@@ -528,15 +554,13 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC554" 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="LC555" 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="LC556" 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="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>
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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>
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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>
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<pre style="margin: 0;">+<span id="LC557" 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="LC558" 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="LC559" 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="LC560" 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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561
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<pre style="margin: 0;">+<span id="LC561" 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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562
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<pre style="margin: 0;">+<span id="LC562" 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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563
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<pre style="margin: 0;">+<span id="LC563" 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="LC564" 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="LC565" class="line" lang="python"></span>
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566
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<pre style="margin: 0;"> <span id="LC566" 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">@@ -551,9 +575,8 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC575" 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="LC576" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC577" 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>
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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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555
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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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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="python"> <span class="p">)</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" 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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579
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<pre style="margin: 0;">+<span id="LC579" 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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557
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580
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<pre style="margin: 0;"> <span id="LC580" 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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558
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581
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<pre style="margin: 0;"> <span id="LC581" 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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559
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<pre style="margin: 0;"> <span id="LC582" 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>
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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">@@ -565,11 +588,9 @@ class _AbstractMapReduceGFF:</td>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC589" 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="LC590" 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="LC591" 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>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="s" style="color: #d14;">"""Provide a collector for local GFF MapReduce file parsing.</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__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="LC595" 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="LC596" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -627,15 +648,13 @@ class _GFFParserLocalOut:</td>
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<pre style="margin: 0;"> <span id="LC648" 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="LC649" 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="LC651" 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="LC652" class="line" lang="python"> <span class="s" style="color: #d14;">"""Local GFF parser providing standardized parsing of GFF3 and GFF2 files.</span></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__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="LC655" 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="LC656" 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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<pre style="margin: 0;">-<span id="LC638" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python"> </span>
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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;">_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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<pre style="margin: 0;"> <span id="LC659" 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="LC660" class="line" lang="python"></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">@@ -665,38 +684,39 @@ class GFFParser(_AbstractMapReduceGFF):</td>
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<pre style="margin: 0;"> <span id="LC684" 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>
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<pre style="margin: 0;"> <span id="LC685" 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>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="python"></span>
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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>
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<pre style="margin: 0;">+<span id="LC687" 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>
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<pre style="margin: 0;">+<span id="LC688" 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="LC689" class="line" lang="python"> <span class="s" style="color: #d14;">"""Generate SeqRecord and SeqFeatures from GFF file lines.</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC691" 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>
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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>
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<pre style="margin: 0;">+<span id="LC692" 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>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;">target_lines</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC694" 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>
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<pre style="margin: 0;"> <span id="LC695" 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>
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<pre style="margin: 0;"> <span id="LC696" 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>
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<pre style="margin: 0;"> <span id="LC697" 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>
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698
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<pre style="margin: 0;"> <span id="LC698" 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>
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678
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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>
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699
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<pre style="margin: 0;">+<span id="LC699" 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>
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<pre style="margin: 0;">+<span id="LC700" 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>
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679
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701
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<pre style="margin: 0;"> <span id="LC701" 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>
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680
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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>
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702
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<pre style="margin: 0;">+<span id="LC702" 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>
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703
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<pre style="margin: 0;">+<span id="LC703" 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>
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704
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<pre style="margin: 0;"> <span id="LC704" 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>
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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>
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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="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>
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<pre style="margin: 0;">+<span id="LC705" 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>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"> <span class="n" style="color: #333;">target_lines</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" 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>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"> <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'FASTA'</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"> <span class="n" style="color: #333;">found_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC712" 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>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC713" 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>
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<pre style="margin: 0;"> <span id="LC714" 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>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC715" 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>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC717" 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>
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<pre style="margin: 0;"> <span id="LC718" 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>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC719" 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>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="python"></span>
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720
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<pre style="margin: 0;"> <span id="LC720" 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>
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<pre style="margin: 0;"> <span id="LC721" 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>
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722
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<pre style="margin: 0;"> <span id="LC722" 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>
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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">@@ -704,7 +724,6 @@ class GFFParser(_AbstractMapReduceGFF):</td>
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<pre style="margin: 0;"> <span id="LC724" 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>
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<pre style="margin: 0;"> <span id="LC725" 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="LC726" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC727" 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>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC729" 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>
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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">@@ -717,11 +736,9 @@ class GFFParser(_AbstractMapReduceGFF):</td>
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<pre style="margin: 0;"> <span id="LC736" 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>
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737
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<pre style="margin: 0;"> <span id="LC737" 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>
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC739" 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>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python"> <span class="s" style="color: #d14;">"""GFF Parser with parallelization through Disco (http://discoproject.org.</span></span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC742" 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>
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="python"> <span class="s" style="color: #d14;">"""Initialize parser.</span></span>
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<pre style="margin: 0;"> <span id="LC744" 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">@@ -738,36 +755,32 @@ class DiscoGFFParser(_AbstractMapReduceGFF):</td>
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># make these imports local; only need them when using disco</span></span>
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">simplejson</span></span>
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">disco</span></span>
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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>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># absolute path names unless they are special disco files<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="python"> <span class="n" style="color: #333;">full_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gff_files</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC761" 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>
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<pre style="margin: 0;"> <span id="LC762" 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>
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<pre style="margin: 0;"> <span id="LC763" 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="LC764" 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>
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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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC765" 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>
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<pre style="margin: 0;">+<span id="LC766" 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>
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<pre style="margin: 0;">+<span id="LC767" 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>
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768
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<pre style="margin: 0;">+<span id="LC768" 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>
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<pre style="margin: 0;">+<span id="LC769" 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>
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<pre style="margin: 0;">+<span id="LC770" 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>
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<pre style="margin: 0;"> <span id="LC771" 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>
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<pre style="margin: 0;"> <span id="LC772" 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>
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773
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<pre style="margin: 0;"> <span id="LC773" 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>
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">processed</span></span>
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC776" 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>
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="python"> <span class="s" style="color: #d14;">"""High level interface to parse GFF files into SeqRecords and SeqFeatures.</span></span>
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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779
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<pre style="margin: 0;"> <span id="LC779" 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="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>
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<pre style="margin: 0;">+<span id="LC780" 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>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python"> <span class="n" style="color: #333;">target_lines</span><span class="p">):</span></span>
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782
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<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>
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC784" 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>
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse GFF files as line by line dictionary of parts.</span></span>
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786
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<pre style="margin: 0;"> <span id="LC786" 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">@@ -784,11 +797,9 @@ def parse_simple(gff_files, limit_info=None):</td>
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784
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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798
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<pre style="margin: 0;"> <span id="LC798" 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>
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="python"></span>
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787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python"></span>
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800
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<pre style="margin: 0;"> <span id="LC800" 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>
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789
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python"> <span class="s" style="color: #d14;">"""Decorator to handle either an input handle or a file.</span></span>
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC803" 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>
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<pre style="margin: 0;"> <span id="LC804" 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>
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805
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<pre style="margin: 0;"> <span id="LC805" 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>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="815" style="width: 35px; color: rgba(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">@@ -804,10 +815,8 @@ def _file_or_handle(fn):</td>
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<pre style="margin: 0;"> <span id="LC815" 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>
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816
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<pre style="margin: 0;"> <span id="LC816" 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>
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out</span></span>
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC818" 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>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC820" 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>
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"> <span class="s" style="color: #d14;">"""Provide high level details about a GFF file to refine parsing.</span></span>
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"></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">@@ -817,22 +826,19 @@ class GFFExaminer:</td>
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"><span class="s" style="color: #d14;"> information you need. This class provides high level summary details to</span></span>
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"><span class="s" style="color: #d14;"> help in learning.</span></span>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC829" 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>
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<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>
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC830" 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>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">gff_source</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">gff_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC833" 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>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="python"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_LocalParams</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC835" 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>
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<pre style="margin: 0;"> <span id="LC836" 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>
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC837" 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>
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">limit_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">limit_info</span></span>
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<pre style="margin: 0;"> <span id="LC839" 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>
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">params</span></span>
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">_file_or_handle</span></span>
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<pre style="margin: 0;"> <span id="LC843" 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>
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<pre style="margin: 0;"> <span id="LC844" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -889,12 +895,16 @@ class GFFExaminer:</td>
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<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</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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<pre style="margin: 0;"> <span id="LC896" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC897" 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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<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>
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893
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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>
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894
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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>
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898
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<pre style="margin: 0;">+<span id="LC898" 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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899
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<pre style="margin: 0;">+<span id="LC899" 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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900
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<pre style="margin: 0;">+<span id="LC900" 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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901
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<pre style="margin: 0;">+<span id="LC901" 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>
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902
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<pre style="margin: 0;">+<span id="LC902" 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>
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903
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<pre style="margin: 0;">+<span id="LC903" 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>
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904
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<pre style="margin: 0;"> <span id="LC904" 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>
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896
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905
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<pre style="margin: 0;"> <span id="LC905" 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>
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897
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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>
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906
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<pre style="margin: 0;">+<span id="LC906" 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>
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<pre style="margin: 0;">+<span id="LC907" 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>
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print parent_sts, child_sts</span></span>
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># generate a dictionary of the unique final type relationships</span></span>
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900
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910
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<pre style="margin: 0;"> <span id="LC910" 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>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#377317303b32a87f51356a964b30d05b7cf78ba3"><strong>BCBio/GFF/__init__.py</strong></a>
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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">@@ -3,4 +3,4 @@</td>
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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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<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>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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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> <span class="s" style="color: #d14;">"0.6.<span class="idiff left right">7</span>"</span></span></pre>
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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> <span class="s" style="color: #d14;">"0.6.<span class="idiff left right">8</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.0</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: bcbio-gff</span>
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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>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.6.<span class="idiff left right">8</span></span>
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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>
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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>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Brad Chapman</span>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#2598951dd9ce972e3fb974dd1069ecb0ac43f16b"><strong>Tests/GFF/hybrid2.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>lcl|chr17</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GATTACA</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">GATTACA</span></pre>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#162c3679ebe63ccaacf9c1837a27f907a63c61a3"><strong>Tests/GFF/hybrid2.gff3</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##gff-version 3</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##sequence-region foo 1 100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##feature-ontology bar</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##attribute-ontology baz</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##source-ontology boo</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##sequence-region chr17 62467934 62469545 </span>
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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>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">chr17 UCSC CDS 62468039 62468236 . - 1 Parent=A00469</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">chr17 UCSC CDS 62468490 62468654 . - 2 Parent=A00469</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">chr17 UCSC CDS 62468747 62468866 . - 1 Parent=A00469</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">chr17 UCSC CDS 62469076 62469236 . - 1 Parent=A00469</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">chr17 UCSC CDS 62469497 62469506 . - 0 Parent=A00469</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">###</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">##FASTA</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">>lcl|chr17</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">GATTACA</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">GATTACA</span></pre>
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<li id="936fbcee4a35275ed493abce9f6c9e7f4180931b">
<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#936fbcee4a35275ed493abce9f6c9e7f4180931b"><strong>Tests/test_GFFSeqIOFeatureAdder.py</strong></a>
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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">@@ -519,6 +519,8 @@ class DirectivesTest(unittest.TestCase):</td>
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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>
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520
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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>
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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>
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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;">_ncbi_gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="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;">"hybrid2.gff3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ncbi_fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="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;">"hybrid2.fa"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC524" 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>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_basic_directives</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="540" style="width: 35px; color: rgba(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="542" style="width: 35px; color: rgba(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">@@ -540,6 +542,24 @@ class DirectivesTest(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">test_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'chr17'</span><span class="p">]</span></span>
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543
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<pre style="margin: 0;"> <span id="LC543" 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>
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_fasta_directive_w_ncbi</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse FASTA sequence information contained in a GFF3 file with NCBI style IDs.</span></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" 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;">_ncbi_fa</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">seq_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="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="LC550" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="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;">_ncbi_gff</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">))</span></span>
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<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;">len</span><span class="p">(</span><span class="n" style="color: #333;">recs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">test_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'lcl|chr17'</span><span class="p">]</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" 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>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_fasta_directive_w_ncbi_fa</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse FASTA sequence information contained in a separate file with NCBI style IDs.</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="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;">_ncbi_gff</span><span class="p">))</span></span>
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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="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>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">test_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="s" style="color: #d14;">'chr17'</span><span class="p">]</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" 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>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">t_examiner_with_fasta</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python"> <span class="s" style="color: #d14;">"""Perform high level examination of files with FASTA directives.</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#788d776bfe907f02f738f7115e219184170cb4f7"><strong>bcbio_gff.egg-info/PKG-INFO</strong></a>
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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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: bcbio-gff</span>
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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>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.6.<span class="idiff left right">8</span></span>
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4
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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>
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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>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Brad Chapman</span>
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<a href="https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/7b0b85cfc0ad17015d0fd9c5a5ef186e6be6d2bf...a0c8f7c5b3bfaa3b3a269bb546b80e7ac84166a8#944df03d39008ed8c63cac4c573db3e9218908ca"><strong>bcbio_gff.egg-info/SOURCES.txt</strong></a>
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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">@@ -21,6 +21,8 @@ Tests/GFF/c_elegans_WS199_shortened_gff.txt</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Tests/GFF/ensembl_gtf.txt</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Tests/GFF/glimmer_nokeyval.gff3</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Tests/GFF/hybrid1.gff3</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Tests/GFF/hybrid2.fa</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Tests/GFF/hybrid2.gff3</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Tests/GFF/jgi_gff2.txt</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Tests/GFF/mouse_extra_comma.gff3</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Tests/GFF/ncbi_gff3.txt</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-bcbio-gff (0.6.8-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version 0.6.8</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Wed, 10 Nov 2021 00:27:07 +0530</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python-bcbio-gff (0.6.7-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version</span>
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