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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/cat-bat">Debian Med / cat-bat</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/301fdafd0b276724fe88b553c07729ac93e1d4dd">301fdafd</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-16T19:30:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/ad70b73a6adea2b09eeb88657efba6c036a247a3">ad70b73a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-16T19:30:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/75178cd962d9bfb9f32e7df98a1c28424351081c">75178cd9</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-16T19:30:45+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.2'
Update to upstream version '5.2'
with Debian dir 9323283c25059db0563395852f42f156bc70f8f9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/4c49ab28c92b914ae09c5f060e38450749d2f320">4c49ab28</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-16T19:30:45+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/632e7d3949cca637b41519f092368fe388fba709">632e7d39</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-16T19:31:27+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix fuzz
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/db35db7db409268c074fc668208abc3d4e4845f2">db35db7d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-16T19:35:12+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/db36fc38e711c5cfeb0e217253368f7d9d0b4b29">db36fc38</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-16T19:35:16+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
CAT_pack/about.py
</a>
</li>
<li class="file-stats">
<a href="#41cb582341a95a9c89a445c128eaf3fe17244ce8">
CAT_pack/add_names.py
</a>
</li>
<li class="file-stats">
<a href="#e8222836be7fdb29f66b8b4d17f23b4258132af6">
CAT_pack/bins.py
</a>
</li>
<li class="file-stats">
<a href="#3bde2f4ee51ad9ed542735d302116cb0044e0701">
CAT_pack/check.py
</a>
</li>
<li class="file-stats">
<a href="#c9605ae03a3a4b82e18359721ef99f78d7cb805d">
CAT_pack/contigs.py
</a>
</li>
<li class="file-stats">
<a href="#6bbeca6e8d1075a4925f51d7fc6bc6fb00da58d2">
CAT_pack/prepare.py
</a>
</li>
<li class="file-stats">
<a href="#d2de8180a93ab5ec1275b60c51b043143321e6de">
CAT_pack/shared.py
</a>
</li>
<li class="file-stats">
<a href="#c8a6fbae43c67e6821811b75dae608fb7b1cd8d0">
CAT_pack/single_bin.py
</a>
</li>
<li class="file-stats">
<a href="#ad331ba5df84e0adc0040e62fd57f4997449759b">
CAT_pack/summarise.py
</a>
</li>
<li class="file-stats">
<a href="#61126ee7b6d7adf8af342e1dc406f7a9cd049438">
CAT_pack/tax.py
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#6365abe88f3afecfc8346965bbb4822915620145">
debian/patches/fix_interpreter.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47"><strong>CAT_pack/about.py</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
</pre>
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3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'F. A. Bastiaan von Meijenfeldt'</span></span>
</pre>
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4
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC4" 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;">'5.<span class="idiff left right">1.</span>2'</span></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">15 July</span>, 2020'</span></span></pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'5.2'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">20 November</span>, 2020'</span></span></pre>
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<li id="41cb582341a95a9c89a445c128eaf3fe17244ce8">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#41cb582341a95a9c89a445c128eaf3fe17244ce8"><strong>CAT_pack/add_names.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" style="width: 35px; color: rgba(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="129" style="width: 35px; color: rgba(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">@@ -129,9 +129,9 @@ def run():</td>
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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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129
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<pre style="margin: 0;"> <span id="LC129" 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;">'#'</span><span class="p">):</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" 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;">rstrip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(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="LC131" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="132" 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="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left right">try</span></span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'lineage'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="python"> <span class="n" style="color: #333;">lineage_index</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;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'lineage'</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="134" 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="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">e<span class="idiff left right">xcept</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">e<span class="idiff left right">lse</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'{0} is not a supported classification file.'</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#e8222836be7fdb29f66b8b4d17f23b4258132af6"><strong>CAT_pack/bins.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">decimal</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">multiprocessing</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(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">@@ -141,7 +140,7 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'no_stars'</span><span class="p">,</span></span>
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142
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC142" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Suppress marking of suggestive <span class="idiff left right">classification</span>s.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Suppress marking of suggestive <span class="idiff left right">taxonomic assignment</span>s.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">'--force'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'force'</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="314" style="width: 35px; color: rgba(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="313" style="width: 35px; color: rgba(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">@@ -314,7 +313,7 @@ def import_bins(bin_folder, bin_suffix, log_file, quiet):</td>
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314
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<pre style="margin: 0;"> <span id="LC313" 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;">bin2contigs</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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315
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1 bin found!'</span></span>
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316
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0} bins found!'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bin2contigs</span><span class="p">))</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0<span class="idiff left right">:,d</span>} bins found!'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bin2contigs</span><span class="p">))</span></span>
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318
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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319
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"></span>
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320
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">bin2contigs</span><span class="p">,</span> <span class="n" style="color: #333;">contig_names</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="569" style="width: 35px; color: rgba(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">@@ -570,7 +569,8 @@ def run():</td>
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570
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"></span>
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571
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bin2classification_output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ORF2LCA_output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf2</span><span class="p">:</span></span>
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572
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# bin</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">classification</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">reason</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage scores</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bin</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bit-score</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bin</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">number of hits</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">top bit-score</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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574
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> </span>
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575
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bin_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">bin2contigs</span><span class="p">):</span></span>
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576
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">LCAs_ORFs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="586" style="width: 35px; color: rgba(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">@@ -586,6 +586,8 @@ def run():</td>
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586
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="python"></span>
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587
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python"></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">n_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ORF2hits</span><span class="p">[</span><span class="n" style="color: #333;">ORF</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="LC591" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python"> <span class="n" style="color: #333;">top_bitscore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_LCA_for_ORF</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">ORF2hits</span><span class="p">[</span><span class="n" style="color: #333;">ORF</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">@@ -593,8 +595,8 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">taxid2parent</span><span class="p">)</span></span>
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxid</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'no taxid found'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">bin_</span><span class="p">,</span> <span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\<span class="idiff left">t</span></span><span class="s" style="color: #d14;"><span class="idiff">{4}</span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span>n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">bin_</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">n_hits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC600" 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="LC601" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_lineage</span><span class="p">(</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC602" 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">@@ -602,14 +604,18 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">star_lineage</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span><span class="p">,</span> <span class="n" style="color: #333;">taxids_with_multiple_offspring</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">bin_</span><span class="p">,</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;">lineage</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="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{4}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">bin_</span><span class="p">,</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">n_hits</span><span class="p">,</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <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;">lineage</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="LC612" class="line" lang="python"> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> </span>
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">LCAs_ORFs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">),)</span></span>
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609
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC616" 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;">LCAs_ORFs</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="LC611" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">unclassified</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">no hits to database</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">no taxid assigned</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">no hits to database</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">''</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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621
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<pre style="margin: 0;"> <span id="LC621" 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">@@ -619,14 +625,14 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">LCAs_ORFs</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"></span>
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineages</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no ORFs with taxids found.'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">unclassifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">no taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"> <span class="s" style="color: #d14;">'hits not found in taxonomy files</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineages</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no lineage whitelisted.'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">unclassifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">no taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"> <span class="s" style="color: #d14;">'no lineage reached minimum bit-score support</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC638" 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">@@ -650,7 +656,7 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># There is only one classification.</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">classifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"> <span class="s" style="color: #d14;">'based on {1}/{2} ORFs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="s" style="color: #d14;">'{3}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"> <span class="s" style="color: #d14;">'{4}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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">@@ -663,7 +669,7 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># There are multiple classifications.</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">classifi</span>ed ({1}/{2})</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">taxid assign</span>ed ({1}/{2})</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python"> <span class="s" style="color: #d14;">'based on {3}/{4} ORFs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"> <span class="s" style="color: #d14;">'{5}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="s" style="color: #d14;">'{6}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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">@@ -676,10 +682,8 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"> <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;">scores</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="LC683" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="python"> <span class="s" style="color: #d14;">'[{0}] BAT is done! {1}/{2} bins classified.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_bins</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="python"> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bin2contigs</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python"> <span class="s" style="color: #d14;">'{0} BAT is done! {1:,d}/{2:,d} bins have taxonomy assigned.'</span></span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">(),</span> <span class="n" style="color: #333;">n_classified_bins</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bin2contigs</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</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;">show_time</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="LC689" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env/ python3</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">hashlib</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</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">@@ -7,6 +8,38 @@ import sys</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shared</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_md5_gz</span><span class="p">(</span><span class="n" style="color: #333;">gz_file</span><span class="p">,</span> <span class="n" style="color: #333;">md5_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Checking file integrity via MD5 checksum.'</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">md5_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">md5_exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</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>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">md5_exp</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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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'WARNING: no MD5 found in {0}. Integrity of {1} can not be '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'established.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">md5_file</span><span class="p">,</span> <span class="n" style="color: #333;">gz_file</span><span class="p">))</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" 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="LC23" class="line" lang="python"> <span class="n" style="color: #333;">md5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">md5</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4096</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">gz_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chunk</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">),</span> <span class="s" style="color: #d14;">b''</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">md5</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">md5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">md5</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">md5</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">md5_exp</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'MD5 of {0} does not check out.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">gz_file</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'MD5 of {0} checks out.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">gz_file</span><span class="p">)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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10
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_memory</span><span class="p">(</span><span class="n" style="color: #333;">Gb</span><span class="p">):</span></span>
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11
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">total_memory</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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12
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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">@@ -138,7 +171,7 @@ def check_bin_folder(bin_folder, bin_suffix, log_file, quiet):</td>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">'WARNING: a single bin is found. You can run BAT in single '</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">'bin mode, with </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">CAT bin</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> as opposed to </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">CAT bins</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> for a '</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">'set of bins. Both modes will give the same results, but you '</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">'might find single mode more convenient for your workflow<span class="idiff left right">!</span>'</span><span class="p">)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">'might find single mode more convenient for your workflow<span class="idiff left right">.</span>'</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</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>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">error</span></span>
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<li id="c9605ae03a3a4b82e18359721ef99f78d7cb805d">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#c9605ae03a3a4b82e18359721ef99f78d7cb805d"><strong>CAT_pack/contigs.py</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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5
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">decimal</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">multiprocessing</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</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">@@ -130,7 +129,7 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'no_stars'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC131" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Suppress marking of suggestive <span class="idiff left right">classification</span>s.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Suppress marking of suggestive <span class="idiff left right">taxonomic assignment</span>s.'</span><span class="p">)</span></span>
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134
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">'--force'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'force'</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">@@ -465,11 +464,12 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">contig2classification_output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ORF2LCA_output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf2</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="s" style="color: #d14;">'# contig</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">classification</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">reason</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage scores</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bit-score</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">number of hits</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">top bit-score</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">contig_names</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contig</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;">contig2ORFs</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;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">unclassifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">no ORFs found</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">no taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">no ORFs found</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">contig</span><span class="p">))</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;">continue</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">@@ -482,14 +482,16 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">n_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ORF2hits</span><span class="p">[</span><span class="n" style="color: #333;">ORF</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">taxid</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;">top_bitscore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_LCA_for_ORF</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"> <span class="n" style="color: #333;">ORF2hits</span><span class="p">[</span><span class="n" style="color: #333;">ORF</span><span class="p">],</span> <span class="n" style="color: #333;">fastaid2LCAtaxid</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxid</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'no taxid found'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\<span class="idiff left">t</span></span><span class="s" style="color: #d14;"><span class="idiff">{3}</span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span>n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">n_hits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC495" 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="LC496" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_lineage</span><span class="p">(</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC497" 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">@@ -497,14 +499,14 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">star_lineage</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span><span class="p">,</span> <span class="n" style="color: #333;">taxids_with_multiple_offspring</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</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;">lineage</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="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\<span class="idiff left">t</span></span><span class="s" style="color: #d14;"><span class="idiff">{3}</span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span>n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">n_hits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </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;">lineage</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="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> </span>
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">LCAs_ORFs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">),)</span></span>
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python"> </span>
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507
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<pre style="margin: 0;"> <span id="LC507" 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;">LCAs_ORFs</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="LC506" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">unclassified</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">no hits to database</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">contig</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">no taxid assigned</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'no hits to database</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">contig</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC512" 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">@@ -514,14 +516,14 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">LCAs_ORFs</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">,</span> <span class="n" style="color: #333;">args</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="LC517" class="line" lang="python"> </span>
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineages</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no ORFs with taxids found.'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">unclassifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">no taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="s" style="color: #d14;">'hits not found in taxonomy files</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">contig</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineages</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no lineage whitelisted.'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">unclassifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">no taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"> <span class="s" style="color: #d14;">'no lineage reached minimum bit-score support</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">contig</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC529" 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">@@ -540,8 +542,8 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC542" 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;">lineages</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="LC543" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># There is only one classification.</span></span>
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}'</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;"><span class="idiff left">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">classifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;"><span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"> <span class="s" style="color: #d14;">'based on {1}/{2} ORFs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"> <span class="s" style="color: #d14;">'{3}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python"> <span class="s" style="color: #d14;">'{4}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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">@@ -554,7 +556,7 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># There are multiple classifications.</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">classifi</span>ed ({1}/{2})</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">taxid assign</span>ed ({1}/{2})</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="s" style="color: #d14;">'based on {3}/{4} ORFs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="s" style="color: #d14;">'{5}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python"> <span class="s" style="color: #d14;">'{6}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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">@@ -566,10 +568,10 @@ def run():</td>
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <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;">lineage</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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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <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;">scores</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="LC570" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;"><span class="idiff left">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">-----------------</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n\n</span></span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">[{0}] CAT is done! {1}/{2} contigs classified.</span>'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">now</span></span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">-----------------</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">{0} CAT is done! {1:,d}/{2:,d} contigs have taxonomy assigned.</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">shared</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">timestamp</span></span><span class="p">(),</span></span>
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_contigs</span><span class="p">,</span></span>
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">contig_names</span><span class="p">)))</span></span>
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#6bbeca6e8d1075a4925f51d7fc6bc6fb00da58d2"><strong>CAT_pack/prepare.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">@@ -17,7 +17,7 @@ import tax</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_arguments</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">date</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">now</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff">date</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">date</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">now</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff">strftime</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">'%Y-%m-%d'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC22" 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;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">prog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'CAT prepare'</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">@@ -125,28 +125,61 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add extra arguments.</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">'date'</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">'min_mem'</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">15</span>0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">'min_mem'</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">20</span>0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">expand_arguments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">memory_bottleneck</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">total_memory</span><span class="p">,</span> <span class="n" style="color: #333;">error</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_memory</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mem</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="s" style="color: #d14;">'at least {0:,d}GB of memory is needed for the database '</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">'construction. {1:,d}GB is found on your system. You can try '</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">'to find a machine with more memory, or download '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">'preconstructed database files from '</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">'tbb.bio.uu.nl/bastiaan/CAT_prepare/.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mem</span><span class="p">,</span> <span class="n" style="color: #333;">total_memory</span><span class="p">))</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">error</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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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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134
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download_taxonomy_files</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/'</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;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Downloading and extracting taxonomy files from {0} to '</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">'taxonomy folder.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">))</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"></span>
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135
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'</span></span>
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136
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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">tmp_taxonomy_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}{1}.taxdump.tar.gz'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">)</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"></span>
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138
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<td class="diff-line-num new_line old" data-linenumber="160" 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="LC138" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Downloading and extracting taxonomy files from {0} to {1}.'</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">taxonomy_folder</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="140" 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">
140
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<td class="diff-line-num new_line old" data-linenumber="160" 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="LC140" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> </span>
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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
142
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_taxonomy_file</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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145
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<td class="diff-line-num new_line old" data-linenumber="163" 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="LC145" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of <span class="idiff left right">taxonomy files failed.'</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of <span class="idiff left">{0} failed.'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">url</span></span><span class="p"><span class="idiff right">)</span></span></span>
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146
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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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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147
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
148
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}.md5'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">md5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}{1}.taxdump.tar.gz.md5'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">md5_file</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of {0} failed.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"></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;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Download complete.'</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_md5_gz</span><span class="p">(</span><span class="n" style="color: #333;">tmp_taxonomy_file</span><span class="p">,</span> <span class="n" style="color: #333;">md5_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>
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150
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tarfile</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp_taxonomy_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tar</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
152
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">tar</span><span class="p">.</span><span class="n" style="color: #333;">extractall</span><span class="p">(</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" style="width: 35px; color: rgba(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="188" style="width: 35px; color: rgba(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">@@ -155,8 +188,8 @@ def download_taxonomy_files(taxonomy_folder, date, log_file, quiet):</td>
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155
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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156
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
157
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"><span class="idiff left right"> </span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" 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">
159
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<td class="diff-line-num new_line old" data-linenumber="191" 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="LC159" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Download complete!</span>'</span></span>
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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"></span>
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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Extracting complete.</span>'</span></span>
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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
160
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<td class="diff-line-num new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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">@@ -164,44 +197,69 @@ def download_taxonomy_files(taxonomy_folder, date, log_file, quiet):</td>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> </span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download_prot_accession2taxid_file</span><span class="p">(</span></span>
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166
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span> <span class="n" style="color: #333;">date</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/'</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="s" style="color: #d14;">'prot.accession2taxid.gz'</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"></span>
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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;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Downloading mapping file from {0} to {1}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">))</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/'</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Downloading mapping file from {0} to taxonomy folder.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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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;">url</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> </span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/'</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">'prot.accession2taxid.FULL.gz'</span><span class="p">)</span></span>
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174
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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175
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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;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">)</span></span>
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176
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of <span class="idiff left right">prot.accession2taxid.gz failed.'</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of <span class="idiff left">{0} failed.'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">url</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
178
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<td class="diff-line-num new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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179
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>
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180
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<td class="diff-line-num new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
181
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="182" 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">
182
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<td class="diff-line-num new_line old" data-linenumber="215" 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="LC182" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Download complete!'</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}.md5'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">md5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}.md5'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">md5_file</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of {0} failed.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Download complete.'</span></span>
</pre>
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183
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> </span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"></span>
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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_md5_gz</span><span class="p">(</span><span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span> <span class="n" style="color: #333;">md5_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"></span>
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187
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"></span>
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188
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">download_nr</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/<span class="idiff left right">nr.gz</span>'</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> </span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">message</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'Downloading nr database from {0} to {1}.'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">url</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">nr_file</span></span><span class="p">)</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/'</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">message</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'Downloading nr database from {0} to database folder.'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">url</span></span><span class="p">)</span></span>
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192
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> </span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz'</span></span>
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194
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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195
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">nr_file</span><span class="p">)</span></span>
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196
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of <span class="idiff left right">nr database failed.'</span></span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of <span class="idiff left">{0} failed.'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">url</span></span><span class="p"><span class="idiff right">)</span></span></span>
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198
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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199
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"></span>
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200
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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201
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"></span>
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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;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Download complete!'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}.md5'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">md5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}.md5'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">)</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">,</span> <span class="n" style="color: #333;">md5_file</span><span class="p">)</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'download of {0} failed.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">url</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Download complete.'</span></span>
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203
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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204
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_md5_gz</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="n" style="color: #333;">md5_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"></span>
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205
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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206
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"></span>
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207
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -213,10 +271,8 @@ def make_diamond_database(</td>
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213
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">'Constructing DIAMOND database {0}.dmnd from {1} using {2} cores. '</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">'Please be patient...'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">diamond_database_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="n" style="color: #333;">nproc</span><span class="p">))</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Constructing DIAMOND database {0}.dmnd from {1} using {2} '</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="s" style="color: #d14;">'cores.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">diamond_database_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="n" style="color: #333;">nproc</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="236" style="width: 35px; color: rgba(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">@@ -236,25 +292,60 @@ def make_diamond_database(</td>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</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="LC239" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'DIAMOND database constructed<span class="idiff left right">!</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'DIAMOND database constructed<span class="idiff left right">.</span>'</span></span>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_prot_accession2taxid</span><span class="p">(</span><span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Loading {0} into memory. Please be patient...'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">)</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_headers_nr</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Loading file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">)</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">fastaid2prot_accessions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">prot_accessions_whitelist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" 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;">f1</span><span class="p">:</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" 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;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"></span>
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315
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<pre style="margin: 0;">+<span id="LC315" 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;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\x01</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">prot_accessions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="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;">line</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">fastaid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prot_accessions</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="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">fastaid2prot_accessions</span><span class="p">[</span><span class="n" style="color: #333;">fastaid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prot_accessions</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">prot_accessions_whitelist</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">prot_accessions</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">fastaid2prot_accessions</span><span class="p">,</span> <span class="n" style="color: #333;">prot_accessions_whitelist</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_prot_accession2taxid</span><span class="p">(</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span> <span class="n" style="color: #333;">prot_accessions_whitelist</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Loading file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">)</span></span>
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248
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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249
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> </span>
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250
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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251
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"></span>
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252
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left">line</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">f1</span></span><span class="p">:</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left">n</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">enumerate</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f1</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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254
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335
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<pre style="margin: 0;"> <span id="LC335" 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;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" 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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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256
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid</span><span class="p">[</span><span class="n" style="color: #333;">line</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="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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337
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<pre style="margin: 0;">+<span id="LC337" 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;">rstrip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</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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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">index_1</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;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'accession.version'</span><span class="p">)</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">index_2</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;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'taxid'</span><span class="p">)</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession</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;">index_1</span><span class="p">]</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prot_accession</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">prot_accessions_whitelist</span><span class="p">:</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid</span><span class="p">[</span><span class="n" style="color: #333;">prot_accession</span><span class="p">]</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;">index_2</span><span class="p">]</span></span>
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258
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"></span>
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259
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">prot_accession2taxid</span></span>
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260
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(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="355" style="width: 35px; color: rgba(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">@@ -264,33 +355,28 @@ def make_fastaid2LCAtaxid_file(</td>
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264
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span></span>
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265
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">nr_file</span><span class="p">,</span></span>
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266
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">taxid2parent</span><span class="p">,</span></span>
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267
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="p">,</span></span>
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268
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">fastaid2prot_accessions</span><span class="p">,</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">prot_accessions_whitelist</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">import_headers_nr</span><span class="p">(</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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269
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">import_prot_accession2taxid</span><span class="p">(</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">log_file</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">quiet</span></span><span class="p"><span class="idiff right">)</span></span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">taxid2parent</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">taxid2rank</span></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">tax</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">import_nodes</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nodes_dmp</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">prot_accessions_whitelist</span></span><span class="p"><span class="idiff right">,</span></span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="idiff left right"> </span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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272
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Finding LCA of all protein accession numbers in fasta headers '</span></span>
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274
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<td class="diff-line-num new_line old" data-linenumber="368" 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="LC274" class="line" lang="python"> <span class="s" style="color: #d14;">'of {0}. Please be patient...'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">))</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Finding LCA of all protein accession numbers in fasta headers.'</span></span>
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275
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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276
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> </span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">no_taxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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277
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">corrected</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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278
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">nr_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf1</span><span class="p">:</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" 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;">f1</span><span class="p">:</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" 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;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span 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;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\x01</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">accession_numbers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="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;">line</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">fastaid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">accession_numbers</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="LC289" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf1</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fastaid</span><span class="p">,</span> <span class="n" style="color: #333;">prot_accessions</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fastaid2prot_accessions</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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290
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">list_of_lineages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left">accession_number</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">accession_number</span>s</span><span class="p">:</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;"><span class="idiff left">prot_accession</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">prot_accession</span>s</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC378" 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="LC293" class="line" lang="python"> <span class="n" style="color: #333;">taxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prot_accession2taxid</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">accession_number</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">taxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prot_accession2taxid</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">prot_accession</span></span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_lineage</span><span class="p">(</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">list_of_lineages</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lineage</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</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">@@ -305,35 +391,38 @@ def make_fastaid2LCAtaxid_file(</td>
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># that are missing in prot.accession2taxid or whose taxid is</span></span>
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306
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># missing in nodes.dmp. NOTE that these entries are thus not</span></span>
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307
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># present in the output file.</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">no_taxid</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="LC395" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">LCAtaxid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_LCA</span><span class="p">(</span><span class="n" style="color: #333;">list_of_lineages</span><span class="p">)</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="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">fastaid</span><span class="p">,</span> <span class="n" style="color: #333;">LCAtaxid</span><span class="p">))</span></span>
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">LCAtaxid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">prot_accession2taxid</span><span class="p">[</span><span class="n" style="color: #333;">fastaid</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">corrected</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="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fastaid</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;">prot_accession2taxid</span> <span class="ow" style="font-weight: 600;">or</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">LCAtaxid</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">prot_accession2taxid</span><span class="p">[</span><span class="n" style="color: #333;">fastaid</span><span class="p">]):</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the fastaid cannot be found in prot.accession2taxid, but</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;"># a taxid is given to the fastaid based on secondary accession</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># numbers, it is counted as a correction as well.</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># numbers, or if the taxid of the header is different from the</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># LCA taxid, it is counted as corrected.</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">corrected</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"></span>
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Done! File {0} is created. '</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="s" style="color: #d14;">'{1} of {2} headers ({3:.1f}%) corrected.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="s" style="color: #d14;">'{1:,d} of {2:,d} headers ({3:.1f}%) corrected. '</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="s" style="color: #d14;">'{4:,d} headers ({5:.1f}%) do not have a taxid assigned.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">corrected</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">total</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">corrected</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">corrected</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">no_taxid</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">no_taxid</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_offspring</span><span class="p">(</span><span class="n" style="color: #333;">nodes_dmp</span><span class="p">,</span> <span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">taxid2parent</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2rank</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">import_nodes</span><span class="p">(</span><span class="n" style="color: #333;">nodes_dmp</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_offspring</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">nodes_dmp</span><span class="p">,</span> <span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Searching nr database for taxids with multiple offspring.'</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC428" 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">@@ -398,7 +487,7 @@ def prepare(step_list, args):</td>
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'download_prot_accession2taxid_file'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">step_list</span><span class="p">:</span></span>
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span></span>
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400
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"> <span class="s" style="color: #d14;">'prot_accession2taxid_file'</span><span class="p">,</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}{1}.prot.accession2taxid.gz'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}{1}.prot.accession2taxid.<span class="idiff left right">FULL.</span>gz'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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402
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">))</span></span>
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403
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"></span>
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404
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"> <span class="n" style="color: #333;">download_prot_accession2taxid_file</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="517" style="width: 35px; color: rgba(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">@@ -428,6 +517,11 @@ def prepare(step_list, args):</td>
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428
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="s" style="color: #d14;">'make_fastaid2LCAtaxid_file'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">step_list</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'make_taxids_with_multiple_offspring_file'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">step_list</span><span class="p">):</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">taxid2parent</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2rank</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">import_nodes</span><span class="p">(</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nodes_dmp</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"></span>
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431
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'make_fastaid2LCAtaxid_file'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">step_list</span><span class="p">:</span></span>
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432
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span></span>
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433
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"> <span class="s" style="color: #d14;">'fastaid2LCAtaxid_file'</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="439" style="width: 35px; color: rgba(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="533" style="width: 35px; color: rgba(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">@@ -439,6 +533,7 @@ def prepare(step_list, args):</td>
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439
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nr_file</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">prot_accession2taxid_file</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;">taxid2parent</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span></span>
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="546" style="width: 35px; color: rgba(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">@@ -451,6 +546,7 @@ def prepare(step_list, args):</td>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"> <span class="n" style="color: #333;">taxid2offspring</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_offspring</span><span class="p">(</span></span>
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nodes_dmp</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fastaid2LCAtaxid_file</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;">taxid2parent</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">write_taxids_with_multiple_offspring_file</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">@@ -460,7 +556,7 @@ def prepare(step_list, args):</td>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left">[{0}] CAT prepare is done!'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">datetime</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">now</span></span><span class="p">()))</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left">{0} CAT prepare is done!'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">shared</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">timestamp</span></span><span class="p">()))</span></span>
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="n" style="color: #333;">show_time</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="LC562" 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">@@ -471,7 +567,7 @@ def prepare(step_list, args):</td>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Supply the following arguments to CAT or BAT if you want to '</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"> <span class="s" style="color: #d14;">'use th<span class="idiff left right">e constructed</span> database:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"> <span class="s" style="color: #d14;">'use th<span class="idiff left right">is</span> database:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="s" style="color: #d14;">'-d / --database_folder {0}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="s" style="color: #d14;">'-t / --taxonomy_folder {1}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">database_folder</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy_folder</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">@@ -545,19 +641,7 @@ def run_fresh(args):</td>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check memory.</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">total_memory</span><span class="p">,</span> <span class="n" style="color: #333;">error</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_memory</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mem</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">error</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;">message</span> <span class="o" style="font-weight: 600;">=</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;">'at least {0}GB of memory is needed for a fresh database '</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="s" style="color: #d14;">'construction. {1}GB is found on your system. You can try to '</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="s" style="color: #d14;">'find a machine with more memory, or download preconstructed '</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"> <span class="s" style="color: #d14;">'database files from '</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="python"> <span class="s" style="color: #d14;">'tbb.bio.uu.nl/bastiaan/CAT_prepare/.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mem</span><span class="p">,</span> <span class="n" style="color: #333;">total_memory</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="python"> <span class="n" style="color: #333;">error</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="LC559" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">memory_bottleneck</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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645
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<pre style="margin: 0;"> <span id="LC645" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"> <span class="n" style="color: #333;">step_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'download_taxonomy_files'</span><span class="p">,</span></span>
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647
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"> <span class="s" style="color: #d14;">'download_prot_accession2taxid_file'</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">@@ -775,20 +859,8 @@ def run_existing(args):</td>
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'make_fastaid2LCAtaxid_file'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">step_list</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check memory.</span></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">total_memory</span><span class="p">,</span> <span class="n" style="color: #333;">error</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_memory</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mem</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="python"> <span class="s" style="color: #d14;">'at least {0}GB of memory is needed for the database '</span></span>
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="python"> <span class="s" style="color: #d14;">'construction. {1}GB is found on your system. You can try '</span></span>
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="python"> <span class="s" style="color: #d14;">'to find a machine with more memory, or download '</span></span>
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="python"> <span class="s" style="color: #d14;">'preconstructed database files '</span></span>
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="python"> <span class="s" style="color: #d14;">'from tbb.bio.uu.nl/bastiaan/CAT_prepare/.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mem</span><span class="p">,</span> <span class="n" style="color: #333;">total_memory</span><span class="p">))</span></span>
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787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python"> <span class="n" style="color: #333;">error</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="LC789" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</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="LC862" class="line" lang="python"> <span class="n" style="color: #333;">memory_bottleneck</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC864" 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;">step_list</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="LC865" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'All necessary files are found. Existing database does not '</span></span>
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="python"> <span class="s" style="color: #d14;">'need any more work...'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#d2de8180a93ab5ec1275b60c51b043143321e6de"><strong>CAT_pack/shared.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">@@ -36,6 +36,13 @@ class SuffixAction(argparse.Action):</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">namespace</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">bin_suffix</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">timestamp</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">str_</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[{0}]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">'%Y-%m-%d %H:%M:%S'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">str_</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">expand_arguments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'r'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="s" style="color: #d14;">'one_minus_r'</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</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">@@ -94,7 +101,12 @@ def explore_taxonomy_folder(args):</td>
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94
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">nodes_dmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}{1}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">)</span></span>
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95
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">file_</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'names.dmp'</span><span class="p">:</span></span>
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96
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">names_dmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}{1}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">)</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'prot.accession2taxid.gz'</span><span class="p">):</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'prot.accession2taxid.FULL.gz'</span><span class="p">):</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}{1}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'prot.accession2taxid.gz'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Legacy prot_accession2taxid_file.</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">prot_accession2taxid_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}{1}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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99
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">taxonomy_folder</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;"> <span id="LC112" 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">@@ -156,15 +168,13 @@ def print_variables(args, step_list=None):</td>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">give_user_feedback</span><span class="p">(</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">message</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">show_time</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;">error</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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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">message</span></span><span class="p"><span class="idiff right">,</span></span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">show_time</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;">error</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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161
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<td class="diff-line-num new_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">
173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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162
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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ERROR: {0}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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163
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>
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164
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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">show_time</span><span class="p">:</span></span>
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165
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<td class="diff-line-num new_line old" data-linenumber="177" 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="LC165" class="line" lang="python"> <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'[{0}] {1}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0} {1}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">timestamp</span><span class="p">(),</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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168
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"></span>
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169
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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170
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" style="width: 35px; color: rgba(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="201" style="width: 35px; color: rgba(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">@@ -191,7 +201,7 @@ def run_prodigal(</td>
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191
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<td class="diff-line-num old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
192
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<td class="diff-line-num new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="s" style="color: #d14;">'Running Prodigal for ORF prediction. Files {0} and {1} will be '</span></span>
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193
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="s" style="color: #d14;">'generated. Do not forget to cite Prodigal when using CAT or BAT '</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="s" style="color: #d14;">'in your publication<span class="idiff left right">!</span>'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">proteins_fasta</span><span class="p">,</span> <span class="n" style="color: #333;">proteins_gff</span><span class="p">))</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">'in your publication<span class="idiff left right">.</span>'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">proteins_fasta</span><span class="p">,</span> <span class="n" style="color: #333;">proteins_gff</span><span class="p">))</span></span>
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195
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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196
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>
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197
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="231" style="width: 35px; color: rgba(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="241" style="width: 35px; color: rgba(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">@@ -231,16 +241,16 @@ def run_diamond(args):</td>
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231
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">'Homology search with DIAMOND is starting. Please be patient. Do '</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="s" style="color: #d14;">'not forget to cite DIAMOND when using CAT or BAT in your '</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"> <span class="s" style="color: #d14;">'publication<span class="idiff left right">!</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">query: {0}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">database: {1}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">mode: {2}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">number of cores: {3}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</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 class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">block-size (billions of letters): {4}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">index-chunks: {5}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">tmpdir: {6}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">compress: {7}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">top: {8}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="s" style="color: #d14;">'publication<span class="idiff left right">.</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">query: {0}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">database: {1}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">mode: {2}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">number of cores: {3}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">block-size (billions of letters): {4}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">index-chunks: {5}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">tmpdir: {6}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">compress: {7}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">top: {8}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">proteins_fasta</span><span class="p">,</span></span>
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">diamond_database</span><span class="p">,</span></span>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">mode</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">@@ -304,9 +314,9 @@ def import_contig_names(fasta_file, log_file, quiet):</td>
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_names</span><span class="p">:</span></span>
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306
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">it looks like your fasta file contains duplicat</span>e '</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">headers! The first duplicate encountered is {0},</span> '</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">but there </span>might be more...'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">contig</span><span class="p">))</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">your fasta file contains duplicate headers. Th</span>e '</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">first duplicate encountered is {0}, but there</span> '</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="s" style="color: #d14;">'might be more...'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">contig</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</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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311
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="369" style="width: 35px; color: rgba(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="379" style="width: 35px; color: rgba(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">@@ -369,14 +379,14 @@ def parse_tabular_alignment(</td>
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369
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ORF</span><span class="p">:</span></span>
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370
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># A new ORF is reached.</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">best</span>_bitscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decimal</span><span class="p">.</span><span class="n" style="color: #333;">Decimal</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">top</span>_bitscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decimal</span><span class="p">.</span><span class="n" style="color: #333;">Decimal</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">ORF2hits</span><span class="p">[</span><span class="n" style="color: #333;">ORF</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">ORF_done</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="LC386" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">bitscore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decimal</span><span class="p">.</span><span class="n" style="color: #333;">Decimal</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bitscore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">one_minus_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">best</span>_bitscore</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bitscore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">one_minus_r</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">top</span>_bitscore</span><span class="p">:</span></span>
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The hit has a high enough bit-score to be included.</span></span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</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="LC392" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">decimal</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">multiprocessing</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</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">@@ -129,7 +128,7 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'no_stars'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC130" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Suppress marking of suggestive <span class="idiff left right">classification</span>s.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Suppress marking of suggestive <span class="idiff left right">taxonomic assignment</span>s.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="s" style="color: #d14;">'--force'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'force'</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">@@ -466,7 +465,8 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bin2classification_output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ORF2LCA_output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf2</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# bin</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">classification</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">reason</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage scores</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bin</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bit-score</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# ORF</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">bin</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">number of hits</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">lineage</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">top bit-score</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The list contains only a single bin, but I keep the code like this</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># to make the code consistent across bin and bins.</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">@@ -484,7 +484,9 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">n_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">ORF2hits</span><span class="p">[</span><span class="n" style="color: #333;">ORF</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">top_bitscore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_LCA_for_ORF</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">ORF2hits</span><span class="p">[</span><span class="n" style="color: #333;">ORF</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">@@ -492,8 +494,8 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">taxid2parent</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">taxid</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'no taxid found'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">bin_</span><span class="p">,</span> <span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\<span class="idiff left">t</span></span><span class="s" style="color: #d14;"><span class="idiff">{4}</span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span>n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">bin_</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">n_hits</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC499" 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="LC500" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">find_lineage</span><span class="p">(</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC501" 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">@@ -501,14 +503,18 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tax</span><span class="p">.</span><span class="n" style="color: #333;">star_lineage</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">lineage</span><span class="p">,</span> <span class="n" style="color: #333;">taxids_with_multiple_offspring</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span> <span class="n" style="color: #333;">bin_</span><span class="p">,</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;">lineage</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="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">outf2</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{2}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{3}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{4}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">ORF</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">bin_</span><span class="p">,</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">n_hits</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="python"> <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;">lineage</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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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">top_bitscore</span><span class="p">))</span></span>
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python"> </span>
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">LCAs_ORFs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">taxid</span><span class="p">,</span> <span class="n" style="color: #333;">top_bitscore</span><span class="p">),)</span></span>
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508
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> </span>
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515
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<pre style="margin: 0;"> <span id="LC515" 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;">LCAs_ORFs</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="LC510" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">unclassified</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">no hits to database</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left">no taxid assigned</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">no hits to database</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">''</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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520
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<pre style="margin: 0;"> <span id="LC520" 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">@@ -518,14 +524,14 @@ def run():</td>
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">LCAs_ORFs</span><span class="p">,</span> <span class="n" style="color: #333;">taxid2parent</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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519
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"> </span>
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineages</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no ORFs with taxids found.'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">unclassifi</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">no taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"> <span class="s" style="color: #d14;">'hits not found in taxonomy files</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineages</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no lineage whitelisted.'</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;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">unclassifi</span>ed</span><span class="se" style="color: #d14;">\t</span><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="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;"><span class="idiff left right">no taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python"> <span class="s" style="color: #d14;">'no lineage reached minimum bit-score support</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">bin_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC537" 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">@@ -549,7 +555,7 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># There is only one classification.</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">classifi</span>ed</span><span class="se" style="color: #d14;">\t</span><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="s" style="color: #d14;">'<span class="idiff left right">taxid assign</span>ed</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"> <span class="s" style="color: #d14;">'based on {1}/{2} ORFs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python"> <span class="s" style="color: #d14;">'{3}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python"> <span class="s" style="color: #d14;">'{4}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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">@@ -562,7 +568,7 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># There are multiple classifications.</span></span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="s" style="color: #d14;">'{0}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">classifi</span>ed ({1}/{2})</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">taxid assign</span>ed ({1}/{2})</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="s" style="color: #d14;">'based on {3}/{4} ORFs</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="s" style="color: #d14;">'{5}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"> <span class="s" style="color: #d14;">'{6}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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">@@ -575,9 +581,8 @@ def run():</td>
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python"> <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;">scores</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="LC582" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">-----------------</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="python"> <span class="s" style="color: #d14;">'[{0}] BAT is done! {1}/1 bin classified.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_bins</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"> <span class="s" style="color: #d14;">'{0} BAT is done! {1}/1 bin has taxonomy assigned.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">(),</span> <span class="n" style="color: #333;">n_classified_bins</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python"> <span class="n" style="color: #333;">show_time</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="LC588" class="line" lang="python"> </span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#ad331ba5df84e0adc0040e62fd57f4997449759b"><strong>CAT_pack/summarise.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">@@ -153,7 +153,7 @@ def summarise_contigs(args):</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">'{0} appears to be a BAT classification file. '</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="s" style="color: #d14;">'If you want to summarise bin '</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">'classifications, simply don</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">t supply a '</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">'contigs fasta and everything should be fine<span class="idiff left right">!</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">'contigs fasta and everything should be fine<span class="idiff left right">.</span>'</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">))</span></span>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">error</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" style="width: 35px; color: rgba(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="182" style="width: 35px; color: rgba(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">@@ -182,7 +182,7 @@ def summarise_contigs(args):</td>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">unclassifi</span>ed'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">no taxid assign</span>ed'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">ORFs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="225" style="width: 35px; color: rgba(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">@@ -225,8 +225,8 @@ def summarise_contigs(args):</td>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"></span>
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC228" 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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'<span class="idiff left right">unclassifi</span>ed'</span><span class="p">:</span></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">unclassifi</span>ed'</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contig2length</span><span class="p">[</span><span class="n" style="color: #333;">contig</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC228" 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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'<span class="idiff left right">no taxid assign</span>ed'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">no taxid assign</span>ed'</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">contig2length</span><span class="p">[</span><span class="n" style="color: #333;">contig</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC232" 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">@@ -270,14 +270,15 @@ def summarise_contigs(args):</td>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">n_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">contig2length</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">total_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">contig2length</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_contigs</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'unclassified'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">total_classified_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'unclassified'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_contigs</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'no taxid assigned'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">total_classified_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">length</span><span class="p">[</span><span class="s" style="color: #d14;">'no taxid assigned'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# total number of contigs in {0} is {1<span class="idiff left right">} representing {2}</span> '</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="s" style="color: #d14;">'positions.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# total number of contigs in {0} is {1<span class="idiff left right">:,d} representing</span> '</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">{2:,d} </span>positions.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">contigs_fasta</span><span class="p">,</span> <span class="n" style="color: #333;">n_contigs</span><span class="p">,</span> <span class="n" style="color: #333;">total_length</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# {0<span class="idiff left right">} contigs are classified ({1:.2f}%) representing {2}</span> '</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="s" style="color: #d14;">'positions ({3:.2f}%) in {4}.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# {0<span class="idiff left right">:,d} contigs have taxonomy assigned ({1:.2f}%)</span> '</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">representing {2:,d} </span>positions ({3:.2f}%) in {4}.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_contigs</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_contigs</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">n_contigs</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span></span>
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">total_classified_length</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">@@ -373,7 +374,7 @@ def summarise_bins(args):</td>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">n_bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">n_bins</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">unclassifi</span>ed'</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="LC377" class="line" lang="python"> <span class="n" style="color: #333;">n_bins</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">no taxid assign</span>ed'</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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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">official_ranks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'superkingdom'</span><span class="p">,</span> <span class="s" style="color: #d14;">'phylum'</span><span class="p">,</span> <span class="s" style="color: #d14;">'class'</span><span class="p">,</span> <span class="s" style="color: #d14;">'order'</span><span class="p">,</span> <span class="s" style="color: #d14;">'family'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="s" style="color: #d14;">'genus'</span><span class="p">,</span> <span class="s" style="color: #d14;">'species'</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">@@ -402,8 +403,8 @@ def summarise_bins(args):</td>
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402
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">bin_trace</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">bin_</span><span class="p">)</span></span>
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC405" 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;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'<span class="idiff left right">unclassifi</span>ed'</span><span class="p">:</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">n_bins</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">unclassifi</span>ed'</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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406
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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;">line</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;">'<span class="idiff left right">no taxid assign</span>ed'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">n_bins</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">no taxid assign</span>ed'</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="LC408" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC410" 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">@@ -427,11 +428,11 @@ def summarise_bins(args):</td>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_bins</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">unclassifi</span>ed'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">n_classified_bins</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_bins</span><span class="p">[</span><span class="s" style="color: #d14;">'<span class="idiff left right">no taxid assign</span>ed'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outf1</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;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# total number of bins is {0<span class="idiff left right">}, of which {1} ({2:.2f}%)</span> '</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">are classifi</span>ed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# total number of bins is {0<span class="idiff left right">:,d}, of which {1:,d}</span> '</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">({2:.2f}%) have taxonomy assign</span>ed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">n_classified_bins</span><span class="p">,</span> <span class="n" style="color: #333;">n_classified_bins</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'#</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">outf1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'# rank</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">clade</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">number of bins</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#61126ee7b6d7adf8af342e1dc406f7a9cd049438"><strong>CAT_pack/tax.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">@@ -6,7 +6,7 @@ import shared</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_nodes</span><span class="p">(</span><span class="n" style="color: #333;">nodes_dmp</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Import</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">nodes_dmp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Load</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">nodes_dmp</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">taxid2parent</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(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="27" style="width: 35px; color: rgba(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">@@ -27,7 +27,7 @@ def import_nodes(nodes_dmp, log_file, quiet):</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_names</span><span class="p">(</span><span class="n" style="color: #333;">names_dmp</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Import</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">names_dmp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Load</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">names_dmp</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">taxid2name</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -46,7 +46,7 @@ def import_names(names_dmp, log_file, quiet):</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_fastaid2LCAtaxid</span><span class="p">(</span><span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">,</span> <span class="n" style="color: #333;">all_hits</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Import</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Load</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">fastaid2LCAtaxid_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">fastaid2LCAtaxid</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">@@ -64,7 +64,7 @@ def import_fastaid2LCAtaxid(fastaid2LCAtaxid_file, all_hits, log_file, quiet):</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">import_taxids_with_multiple_offspring</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">taxids_with_multiple_offspring_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Import</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">taxids_with_multiple_offspring_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">Load</span>ing file {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">taxids_with_multiple_offspring_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">give_user_feedback</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">taxids_with_multiple_offspring</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</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">@@ -251,7 +251,7 @@ def convert_to_official_names(lineage, taxid2rank, taxid2name, scores=None):</td>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">'genus'</span><span class="p">,</span> <span class="s" style="color: #d14;">'species'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">lineage_ranks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">taxid2rank</span><span class="p">[</span><span class="n" style="color: #333;">taxid</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'*'</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">taxid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineage</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">official_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'no<span class="idiff left right">t classified</span>'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">7</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">official_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'no<span class="idiff left right"> support</span>'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">7</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"></span>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">rank</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">official_ranks</span><span class="p">):</span></span>
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rank</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineage_ranks</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" style="width: 35px; color: rgba(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="282" style="width: 35px; color: rgba(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">@@ -282,11 +282,11 @@ def convert_to_official_names(lineage, taxid2rank, taxid2name, scores=None):</td>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Fill the official lineage with NAs if a lower classification is present.</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">index_lowest_classification</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="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">official_names</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'no<span class="idiff left right">t classified</span>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'no<span class="idiff left right"> support</span>'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">index_lowest_classification</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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<pre style="margin: 0;"> <span id="LC287" 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;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">index_lowest_classification</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">official_names</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no<span class="idiff left right">t classified</span>'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">official_names</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no<span class="idiff left right"> support</span>'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">official_names</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'NA'</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">official_names</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changelog</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 5.2</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="sb" style="color: #d14;">`CAT prepare`</span> now uses the latest taxonomy mapping files from NCBI, significantly expanding taxonomic coverage of proteins in nr. File integrity of downloads is assessed based on md5 checksums. The ORF2LCA output file contains a new column for the number of hits the classification is based on. We have made textual changes to the output files to better reflect the meaning of 'classified' and 'not classified' in different contexts.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 5.1.2</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">Code streamlining.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></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">@@ -6,7 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Getting started</span><span class="p">](</span><span class="sx" style="color: #d14;">#getting-started</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#usage</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Interpreting the output files</span><span class="p">](</span><span class="sx" style="color: #d14;">#interpreting-the-output-files</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Marking suggestive <span class="idiff left">classifications with an asterisk</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">#marking-suggestive-classification</span>s-with-an-asterisk</span><span class="p">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Marking suggestive <span class="idiff left">taxonomic assignments with an asterisk</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">#marking-suggestive-taxonomic-assignment</span>s-with-an-asterisk</span><span class="p">)</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Optimising running time, RAM, and disk usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#optimising-running-time-ram-and-disk-usage</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Examples</span><span class="p">](</span><span class="sx" style="color: #d14;">#examples</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></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">@@ -55,15 +55,15 @@ To get started with CAT and BAT, you will have to get the database files on your</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown">To download the database files, find the most recent version on <span class="p">[</span><span class="nv" style="color: #008080;">tbb.bio.uu.nl/bastiaan/CAT\_prepare/</span><span class="p">](</span><span class="sx" style="color: #d14;">https://tbb.bio.uu.nl/bastiaan/CAT_prepare/</span><span class="p">)</span>, download and extract, and you are ready to go!</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown">$ wget tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_2020<span class="idiff left right">0618</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">$ wget tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_2020<span class="idiff left right">1123</span>.tar.gz</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">$ tar -xvzf CAT_prepare_2020<span class="idiff left right">0618</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown">$ tar -xvzf CAT_prepare_2020<span class="idiff left right">1123</span>.tar.gz</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"><span class="idiff left right">Make sure that your version of DIAMOND is the same as with which the database is constructed. You can find the DIAMOND vers</span>ion within the database log file:</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="idiff left right">Your version of DIAMOND should be the same as with which the database is constructed. For this reason the DIAMOND executable is supplied within the CAT prepare folder. Alternatively, you can find the DIAMOND version used for database construct</span>ion within the database log file:</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown">$ grep version 2020-<span class="idiff left right">06-18</span>.CAT_prepare.fresh.log</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown">$ grep version 2020-<span class="idiff left right">11-23</span>.CAT_prepare.fresh.log</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Generating the database files yourself.</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">@@ -72,14 +72,14 @@ $ grep version 2020-06-18.CAT_prepare.fresh.log</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown">$ CAT prepare --fresh</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown">This will download the taxonomy files from NCBI taxonomy to a taxonomy folder, and the nr database to a database folder. A DIAMOND database is constructed from the nr file. CAT prepare also generates a fastaid2LCAtaxid file, as the first accession numbers in the headers of nr are not necessarily the Last Common Ancestor (LCA) of all accession numbers in it. Moreover, the file taxids<span class="se" style="color: #d14;">\_</span>with<span class="se" style="color: #d14;">\_</span>multiple<span class="se" style="color: #d14;">\_</span>offspring is generated. CAT prepare will typically take a few hours to create a fresh database, and will use up to <span class="idiff left right">1</span>00GB of memory.</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown">This will download the taxonomy files from NCBI taxonomy to a taxonomy folder, and the nr database to a database folder. A DIAMOND database is constructed from the nr file. CAT prepare also generates a fastaid2LCAtaxid file, as the first accession numbers in the headers of nr are not necessarily the Last Common Ancestor (LCA) of all accession numbers in it. Moreover, the file taxids<span class="se" style="color: #d14;">\_</span>with<span class="se" style="color: #d14;">\_</span>multiple<span class="se" style="color: #d14;">\_</span>offspring is generated. CAT prepare will typically take a few hours to create a fresh database, and will use up to <span class="idiff left right">2</span>00GB of memory.</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown">If some of the files are already on your system (say the taxonomy files and the nr database) you can run:</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown">$ CAT prepare --existing -d {folder containing nr} -t {folder containing taxonomy files}</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown">CAT prepare will <span class="idiff left right">try to </span>assess which files need to be downloaded and created and start from that point. CAT prepare only checks if the necessary files are there, not if they are correctly formatted.</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown">CAT prepare will assess which files need to be downloaded and created and start from that point. CAT prepare only checks if the necessary files are there, not if they are correctly formatted.</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Running CAT and BAT.</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown">The taxonomy folder and database folder created by CAT prepare are needed in subsequent CAT and BAT runs. They only need to be generated/downloaded once or whenever you want to update the nr database.</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">@@ -157,12 +157,12 @@ The contig2classification and bin2classification output looks like this:</td>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown">contig or bin | classification | reason | lineage | lineage scores</span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown">--- | --- | --- | --- | ---</span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>1 | <span class="idiff left right">classifi</span>ed | based on 14/15 ORFs | 1;131567;2;1783272 | 1.00; 1.00; 1.00; 0.78</span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>2 | <span class="idiff left right">classifi</span>ed (1/2) | based on 10/10 ORFs | 1;131567;2;1783272;1798711;1117;307596;307595;1890422;33071;1416614;1183438<span class="se" style="color: #d14;">\*</span> | 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.23;0.23</span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>2 | <span class="idiff left right">classifi</span>ed (2/2) | based on 10/10 ORFs | 1;131567;2;1783272;1798711;1117;307596;307595;1890422;33071;33072 | 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.77</span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>3 | <span class="idiff left right">unclassifi</span>ed | no ORFs found</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>1 | <span class="idiff left right">taxid assign</span>ed | based on 14/15 ORFs | 1;131567;2;1783272 | 1.00; 1.00; 1.00; 0.78</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>2 | <span class="idiff left right">taxid assign</span>ed (1/2) | based on 10/10 ORFs | 1;131567;2;1783272;1798711;1117;307596;307595;1890422;33071;1416614;1183438<span class="se" style="color: #d14;">\*</span> | 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.23;0.23</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>2 | <span class="idiff left right">taxid assign</span>ed (2/2) | based on 10/10 ORFs | 1;131567;2;1783272;1798711;1117;307596;307595;1890422;33071;33072 | 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;0.77</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown">contig<span class="se" style="color: #d14;">\_</span>3 | <span class="idiff left right">no taxid assign</span>ed | no ORFs found</span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="markdown">Where the lineage scores represent the fraction of bit-score support for each classification. <span class="gs" style="font-weight: 600;">**Contig\_2 has two classifications.**</span> This can happen if the <span class="ge" style="font-style: italic;">*f*</span> parameter is chosen below 0.5. For an explanation of the <span class="gs" style="font-weight: 600;">**starred classification**</span>, see <span class="p">[</span><span class="nv" style="color: #008080;">Marking suggestive <span class="idiff left">classifications with an asterisk</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">#marking-suggestive-classification</span>s-with-an-asterisk</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown">Where the lineage scores represent the fraction of bit-score support for each classification. <span class="gs" style="font-weight: 600;">**Contig\_2 has two classifications.**</span> This can happen if the <span class="ge" style="font-style: italic;">*f*</span> parameter is chosen below 0.5. For an explanation of the <span class="gs" style="font-weight: 600;">**starred classification**</span>, see <span class="p">[</span><span class="nv" style="color: #008080;">Marking suggestive <span class="idiff left">taxonomic assignments with an asterisk</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">#marking-suggestive-taxonomic-assignment</span>s-with-an-asterisk</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="markdown">To add names to the taxonomy id's in either output file, run:</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">@@ -192,8 +192,8 @@ $ CAT summarise -i {named BAT classification file} -o {output file}</td>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown">CAT summarise currently does not support classification files wherein some contigs / MAGs have multiple classifications (as contig<span class="se" style="color: #d14;">\_</span>2 above).</span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Marking suggestive <span class="idiff left right">classification</span>s with an asterisk</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="markdown">When we want to confidently go down to the lowest taxonomic level possible for a<span class="idiff left right">n</span> classification, an important assumption is that on that level conflict between classifications could have arisen. Namely, if there were conflicting classifications, the algorithm would have made the classification more conservative by moving up a level. Since it did not, we can trust the low-level classification. However, it is not always possible for conflict to arise, because in some cases no other sequences from the clade are present in the database. This is true for example for the family Dehalococcoidaceae, which in our databases is the sole representative of the order Dehalococcoidales. Thus, here we cannot confidently state that an classification on the family level is more correct than an classification on the order level. For these cases, CAT and BAT mark the lineage with asterisks, starting from the lowest level classification up to the level where conflict could have arisen because the clade contains multiple taxa with database entries. The user is advised to examine starred taxa more carefully, for example by analysing sequence identity between predicted ORFs and hits, or move up the lineage to a confident classification (i.e. the first classification without an asterisk).</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Marking suggestive <span class="idiff left right">taxonomic assignment</span>s with an asterisk</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown">When we want to confidently go down to the lowest taxonomic level possible for a classification, an important assumption is that on that level conflict between classifications could have arisen. Namely, if there were conflicting classifications, the algorithm would have made the classification more conservative by moving up a level. Since it did not, we can trust the low-level classification. However, it is not always possible for conflict to arise, because in some cases no other sequences from the clade are present in the database. This is true for example for the family Dehalococcoidaceae, which in our databases is the sole representative of the order Dehalococcoidales. Thus, here we cannot confidently state that an classification on the family level is more correct than an classification on the order level. For these cases, CAT and BAT mark the lineage with asterisks, starting from the lowest level classification up to the level where conflict could have arisen because the clade contains multiple taxa with database entries. The user is advised to examine starred taxa more carefully, for example by analysing sequence identity between predicted ORFs and hits, or move up the lineage to a confident classification (i.e. the first classification without an asterisk).</span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="markdown">If you do not want the asterisks in your output files, you can add the <span class="sb" style="color: #d14;">`--no_stars`</span> flag to CAT or BAT.</span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cat-bat (5.2-1) 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"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</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 <npatra974@gmail.com> Wed, 16 Dec 2020 19:31:44 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">cat-bat (5.1.2-1) 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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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: cat-bat</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org><span class="idiff left right">, Nilesh Patra <npatra974@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> diamond-aligner</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/cat-bat</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/cat-bat.git</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://github.com/dutilh/CAT</span>
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<li id="6365abe88f3afecfc8346965bbb4822915620145">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/e860a73ba7c64a5a844845c0c1318cf3907e0dbe...db36fc38e711c5cfeb0e217253368f7d9d0b4b29#6365abe88f3afecfc8346965bbb4822915620145"><strong>debian/patches/fix_interpreter.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,5 +8,5 @@ Description: Fix typo in interpreter line</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env/ python3</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import hashlib</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> import os</span></pre>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> import subprocess</span></pre>
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