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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/aa8acaa0a0454b1a099a39a806827cd1e0d9215b">aa8acaa0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T19:46:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.2.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/5ce505402df6ba4c7ca36109b9da8564059c07a4">5ce50540</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T19:46:02+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/255cb6e1871057698fccff797d9954c78764617a">255cb6e1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T19:46:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.2.2'
Update to upstream version '5.2.2'
with Debian dir 0fb638a1854366ee06085fe11931b501fdd9721d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/6f64ab3fabc3db4355fafb5864c66ed4585a7977">6f64ab3f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-18T19:46:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a879d58e10d9eb09da40178dd663fbc1b1f873c7">
CAT_pack/CAT
</a>
</li>
<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
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</li>
<li class="file-stats">
<a href="#d2de8180a93ab5ec1275b60c51b043143321e6de">
CAT_pack/shared.py
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</li>
<li class="file-stats">
<a href="#c8a6fbae43c67e6821811b75dae608fb7b1cd8d0">
CAT_pack/single_bin.py
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</li>
<li class="file-stats">
<a href="#ad331ba5df84e0adc0040e62fd57f4997449759b">
CAT_pack/summarise.py
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="a879d58e10d9eb09da40178dd663fbc1b1f873c7">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#a879d58e10d9eb09da40178dd663fbc1b1f873c7"><strong>CAT_pack/CAT</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" style="width: 35px; color: rgba(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="39" style="width: 35px; color: rgba(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">@@ -39,7 +39,7 @@ def help():</td>
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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'Run Contig Annotation Tool (CAT) or '</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
40
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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'Bin Annotation Tool (BAT).</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">'</span></span>
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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
41
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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'Required choice:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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42
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<td class="diff-line-num new_line old" data-linenumber="42" 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="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">' prepare</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;"><span class="idiff left right">Download database files and construct databas</span>es.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">' prepare</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;"><span class="idiff left right">Construct database fil</span>es.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
43
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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">' contigs</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Run CAT.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">' bin</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Run BAT on a single bin.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">' bins</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">Run BAT on a set of bins.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
</pre>
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<li id="6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47"><strong>CAT_pack/about.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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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="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>
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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 class="idiff left right">1</span>'</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">6</span> January, 2021'</span></span></pre>
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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 class="idiff left right">2</span>'</span></span>
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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">15</span> January, 2021'</span></span></pre>
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<li id="41cb582341a95a9c89a445c128eaf3fe17244ce8">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#41cb582341a95a9c89a445c128eaf3fe17244ce8"><strong>CAT_pack/add_names.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">@@ -17,70 +17,18 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">add_help</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="LC18" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'-i'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'--input_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" 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;">'input_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to input file. Can be either classification output '</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">'file or ORF2LCA output file.'</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;">required</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="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'--output_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC34" 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;">'output_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" 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;">'Path to output file.'</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;">required</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="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'--taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">'taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to folder that contains taxonomy files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'input_file'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">help_</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to input file. Can be classification or ORF2LCA '</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'output file from CAT or BAT.'</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'output_file'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'taxonomy_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Optional arguments'</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;">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="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'--only_official'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC54" 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;">'only_official'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" 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="LC56" 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="LC57" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Only output official rank names (i.e., superkingdom, '</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">'phylum, class, order, family, genus, species).'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC59" 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="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">'--exclude_scores'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC61" 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;">'exclude_scores'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC62" 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="LC63" 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="LC64" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Do not include bit-score support scores in the lineage of '</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">'a classification output file.'</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;">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="LC67" 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="LC68" 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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<pre style="margin: 0;">-<span id="LC69" 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="LC70" 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="LC71" 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;">'Force overwrite existing files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC72" 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="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC75" 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;">'quiet'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC76" 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="LC77" 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="LC78" 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 verbosity.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC79" 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="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">'-h'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="s" style="color: #d14;">'--help'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC82" 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;">'help'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC83" 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;">'Show this help message and exit.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'only_official'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'exclude_scores'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'force'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'help'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">extra_args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" style="width: 35px; color: rgba(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">@@ -113,6 +61,10 @@ def run():</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_output_file</span><span class="p">(</span></span>
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114
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <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="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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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">errors</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_in_and_output_file</span><span class="p">(</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <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 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="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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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">True</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">errors</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC69" 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="LC70" class="line" lang="python"></span>
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<li id="e8222836be7fdb29f66b8b4d17f23b4258132af6">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#e8222836be7fdb29f66b8b4d17f23b4258132af6"><strong>CAT_pack/bins.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">@@ -18,230 +18,43 @@ def parse_arguments():</td>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Run Bin Annotation Tool (BAT) on a set of bins.'</span><span class="p">,</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'CAT bins -b -d -t [options] [-h / --help]'</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;">add_help</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="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;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required arguments'</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="LC24" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'-b'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'--bin_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" 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;">'bin_folder'</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;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC32" 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;">'Path to directory containing bins.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'-d'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'--database_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to folder that contains database files.'</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;">required</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="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'--taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" 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;">'taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to folder that contains taxonomy files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required arguments'</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'bin_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'database_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'taxonomy_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Optional arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC53" 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="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'-s'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">'--bin_suffix'</span><span class="p">,</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" 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;">'bin_suffix'</span><span class="p">,</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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58
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<pre style="margin: 0;">-<span id="LC58" 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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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'.fna'</span><span class="p">,</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" 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;">'Suffix of bins in bin folder (default: .fna).'</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" 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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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">'--range'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC65" 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;">'r'</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;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC67" 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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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">)],</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">default</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="mi" style="color: #099;">5</span><span class="p">),</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" 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;">'r parameter [0-49] (default: 5).'</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" 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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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">'-f'</span><span class="p">,</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">'--fraction'</span><span class="p">,</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'f'</span><span class="p">,</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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78
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<pre style="margin: 0;">-<span id="LC78" 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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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)],</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">default</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="mf" style="color: #099;">0.3</span><span class="p">),</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" 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;">'f parameter [0-0.99] (default: 0.3).'</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" 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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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'--out_prefix'</span><span class="p">,</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" 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;">'out_prefix'</span><span class="p">,</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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89
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<pre style="margin: 0;">-<span id="LC89" 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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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./out.BAT'</span><span class="p">,</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" 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;">'Prefix for output files (default: out.BAT).'</span><span class="p">)</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" 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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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="s" style="color: #d14;">'-p'</span><span class="p">,</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">'--proteins_fasta'</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="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'proteins_fasta'</span><span class="p">,</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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99
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<pre style="margin: 0;">-<span id="LC99" 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="LC100" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to concatenated predicted proteins fasta file '</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">'generated during an earlier run of BAT. If supplied, BAT '</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">'will skip the protein prediction step.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC105" 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="LC106" class="line" lang="python"> <span class="s" style="color: #d14;">'-a'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'--diamond_alignment'</span><span class="p">,</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'alignment_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC110" 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="LC111" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to alignment table generated during an earlier run of '</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="s" style="color: #d14;">'BAT. If supplied, BAT will skip the alignment step and '</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">'directly classify the bins. A concatenated predicted '</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">'proteins fasta file should also be supplied with argument '</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">'[-p / --proteins].'</span><span class="p">))</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" 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="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_prodigal'</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" 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;">'path_to_prodigal'</span><span class="p">,</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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122
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<pre style="margin: 0;">-<span id="LC122" 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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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'prodigal'</span><span class="p">,</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to Prodigal binaries. Supply if BAT can not find '</span></span>
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<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'Prodigal.'</span><span class="p">))</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" 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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<td class="diff-line-num old old_line" data-linenumber="129" 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">
129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_diamond'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'path_to_diamond'</span><span class="p">,</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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132
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<pre style="margin: 0;">-<span id="LC132" 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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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to DIAMOND binaries. Supply if BAT can not find '</span></span>
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<td class="diff-line-num old old_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="s" style="color: #d14;">'DIAMOND.'</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">-<span id="LC138" 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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<td class="diff-line-num old old_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_stars'</span><span class="p">,</span></span>
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140
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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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<td class="diff-line-num old old_line" data-linenumber="141" 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">
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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<td class="diff-line-num old old_line" data-linenumber="142" 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">
142
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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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<td class="diff-line-num old old_line" data-linenumber="143" 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">
143
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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 taxonomic assignments.'</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="144" 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">
144
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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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146
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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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147
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<pre style="margin: 0;">-<span id="LC147" 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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148
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<pre style="margin: 0;">-<span id="LC148" 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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149
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<pre style="margin: 0;">-<span id="LC149" 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;">'Force overwrite existing files.'</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" 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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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</span><span class="p">,</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="s" style="color: #d14;">'--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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">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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155
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<pre style="margin: 0;">-<span id="LC155" 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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156
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<pre style="margin: 0;">-<span id="LC156" 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 verbosity.'</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 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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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="s" style="color: #d14;">'--verbose'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'verbose'</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;">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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161
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<pre style="margin: 0;">-<span id="LC161" 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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162
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<pre style="margin: 0;">-<span id="LC162" 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;">'Increase verbosity.'</span><span class="p">)</span></span>
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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;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_log'</span><span class="p">,</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'no_log'</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 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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167
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<pre style="margin: 0;">-<span id="LC167" 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="LC168" 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 log file.'</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 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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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">'-h'</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="s" style="color: #d14;">'--help'</span><span class="p">,</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'help'</span><span class="p">,</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show this help message and exit.'</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="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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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">'--I_know_what_Im_doing'</span><span class="p">,</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'IkwId'</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;">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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178
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<pre style="margin: 0;">-<span id="LC178" 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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179
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<pre style="margin: 0;">-<span id="LC179" 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;">'Flag for experimental features.'</span><span class="p">)</span></span>
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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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'bin_suffix'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'.fna'</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="mi" style="color: #099;">5</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 class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="mf" style="color: #099;">0.3</span><span class="p">))</span></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="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'out_prefix'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./out.BAT'</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'proteins_fasta'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">help_</span><span class="o" style="font-weight: 600;">=</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 class="s" style="color: #d14;">'Path to concatenated predicted proteins fasta file '</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'generated during an earlier run of BAT on the same bins. If '</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">'supplied, BAT will skip the protein prediction step.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'alignment_file'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">help_</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">'Path to alignment table generated during an earlier run of '</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'BAT on the same bins. If supplied, BAT will skip the '</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'alignment step and directly classify the bins. A '</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'concatenated predicted proteins fasta file should also be '</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'supplied with argument [-p / --proteins].'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'path_to_prodigal'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'prodigal'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'path_to_diamond'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_stars'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'force'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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50
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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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'verbose'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_log'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'help'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'IkwId'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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181
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">specific</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND specific optional arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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 class="s" style="color: #d14;">'-n'</span><span class="p">,</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="s" style="color: #d14;">'--nproc'</span><span class="p">,</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" 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;">'nproc'</span><span class="p">,</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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188
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<pre style="margin: 0;">-<span id="LC188" 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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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">(),</span></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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Number of cores to deploy by DIAMOND (default: maximum).'</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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 class="s" style="color: #d14;">'--sensitive'</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 class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sensitive'</span><span class="p">,</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" 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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196
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<pre style="margin: 0;">-<span id="LC196" 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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197
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<pre style="margin: 0;">-<span id="LC197" 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;">'Run DIAMOND in sensitive mode (default: not enabled).'</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<td class="diff-line-num old old_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">'--block_size'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'block_size'</span><span class="p">,</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;">metavar</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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202
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<pre style="margin: 0;">-<span id="LC202" 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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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</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="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2.0</span><span class="p">,</span></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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND block-size parameter (default: 2.0). Lower numbers '</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">'will decrease memory and temporary disk space usage.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC208" class="line" lang="python"> <span class="s" style="color: #d14;">'--index_chunks'</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'index_chunks'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC211" 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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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND index-chunks parameter (default: 4). Set to 1 on '</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="s" style="color: #d14;">'high memory machines. The parameter has no effect on '</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">'temporary disk space usage.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">'--tmpdir'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'tmpdir'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC221" 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="LC222" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Directory for temporary DIAMOND files (default: directory '</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="s" style="color: #d14;">'to which output files are written).'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">'--compress'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC228" 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;">'compress'</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;">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="LC230" 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="LC231" 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;">'Compress DIAMOND alignment file.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC233" class="line" lang="python"> <span class="s" style="color: #d14;">'--top'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC234" 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;">'top'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC236" 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="LC237" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">51</span><span class="p">)],</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND top parameter [0-50] (default: 50). Governs hits '</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="s" style="color: #d14;">'within range of best hit that are written to the alignment '</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">'file. This is not the [-r / --range] parameter! Can only be '</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="s" style="color: #d14;">'set with the [--I_know_what_Im_doing] flag, see README.md.'</span><span class="p">))</span></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="LC56" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_all_diamond_arguments</span><span class="p">(</span><span class="n" style="color: #333;">specific</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">extra_args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></span>
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246
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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247
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">extra_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">arg</span> <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;">arg</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;">extra_args</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#3bde2f4ee51ad9ed542735d302116cb0044e0701"><strong>CAT_pack/check.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">@@ -276,6 +276,18 @@ def check_input_file(input_file, log_file, quiet):</td>
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<pre style="margin: 0;"> <span id="LC276" 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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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></span>
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_in_and_output_file</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">output_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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280
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<pre style="margin: 0;">+<span id="LC280" 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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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"></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="n" style="color: #333;">input_file</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">output_file</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="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'input file and output file can not be the same.'</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;">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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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="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;">return</span> <span class="n" style="color: #333;">error</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="LC290" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_top</span><span class="p">(</span><span class="n" style="color: #333;">top</span><span class="p">,</span> <span class="n" style="color: #333;">r</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="LC292" 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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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#c9605ae03a3a4b82e18359721ef99f78d7cb805d"><strong>CAT_pack/contigs.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">@@ -2,7 +2,6 @@</td>
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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>
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3
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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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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">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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<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;">sys</span></span>
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6
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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 class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">about</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">@@ -19,218 +18,30 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">add_help</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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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'-c'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'--contigs_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" 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;">'contigs_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to contigs fasta file.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'-d'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'--database_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" 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;">'database_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to folder that contains database files.'</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;">required</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="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'--taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" 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;">'taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to folder that contains taxonomy files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'contigs_fasta'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'database_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'taxonomy_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</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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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Optional arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC53" 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="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">'--range'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC56" 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;">'r'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC58" 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="LC59" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">)],</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">default</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="mi" style="color: #099;">10</span><span class="p">),</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" 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;">'r parameter [0-49] (default: 10).'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">'-f'</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">'--fraction'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'f'</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;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" 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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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)],</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">default</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="mf" style="color: #099;">0.5</span><span class="p">),</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" 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;">'f parameter [0-0.99] (default: 0.5).'</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" 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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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">'--out_prefix'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC78" 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;">'out_prefix'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC80" 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="LC81" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./out.CAT'</span><span class="p">,</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" 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;">'Prefix for output files (default: out.CAT).'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC85" 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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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'-p'</span><span class="p">,</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">'--proteins_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC88" 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;">'proteins_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC90" 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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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to predicted proteins fasta file. If supplied, CAT '</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'will skip the protein prediction step.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC95" 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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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">'-a'</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="s" style="color: #d14;">'--diamond_alignment'</span><span class="p">,</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" 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;">'alignment_file'</span><span class="p">,</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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100
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<pre style="margin: 0;">-<span id="LC100" 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="LC101" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to alignment table. If supplied, CAT will skip the '</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">'alignment step and directly classify the contigs. A '</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">'predicted proteins fasta file should also be supplied with '</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="s" style="color: #d14;">'argument [-p / --proteins].'</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="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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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_prodigal'</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="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'path_to_prodigal'</span><span class="p">,</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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111
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<pre style="margin: 0;">-<span id="LC111" 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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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'prodigal'</span><span class="p">,</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to Prodigal binaries. Supply if CAT can not find '</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">'Prodigal.'</span><span class="p">))</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" 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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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_diamond'</span><span class="p">,</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" 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;">'path_to_diamond'</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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121
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<pre style="margin: 0;">-<span id="LC121" 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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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</span><span class="p">,</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to DIAMOND binaries. Supply if CAT can not find '</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">'DIAMOND.'</span><span class="p">))</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" 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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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_stars'</span><span class="p">,</span></span>
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129
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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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130
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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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131
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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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132
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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 taxonomic assignments.'</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;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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134
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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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135
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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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<pre style="margin: 0;">-<span id="LC136" 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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137
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<pre style="margin: 0;">-<span id="LC137" 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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138
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<pre style="margin: 0;">-<span id="LC138" 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;">'Force overwrite existing files.'</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" 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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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</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 class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" 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;">'quiet'</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;">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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144
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<pre style="margin: 0;">-<span id="LC144" 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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145
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<pre style="margin: 0;">-<span id="LC145" 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 verbosity.'</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 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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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">'--verbose'</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 class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'verbose'</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 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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150
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<pre style="margin: 0;">-<span id="LC150" 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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151
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<pre style="margin: 0;">-<span id="LC151" 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;">'Increase verbosity.'</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" 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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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_log'</span><span class="p">,</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'no_log'</span><span class="p">,</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" 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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156
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<pre style="margin: 0;">-<span id="LC156" 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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157
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<pre style="margin: 0;">-<span id="LC157" 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 log file.'</span><span class="p">)</span></span>
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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;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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="s" style="color: #d14;">'-h'</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="s" style="color: #d14;">'--help'</span><span class="p">,</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" 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;">'help'</span><span class="p">,</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" 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;">'Show this help message and exit.'</span><span class="p">)</span></span>
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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;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="s" style="color: #d14;">'--I_know_what_Im_doing'</span><span class="p">,</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'IkwId'</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 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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167
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<pre style="margin: 0;">-<span id="LC167" 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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168
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<pre style="margin: 0;">-<span id="LC168" 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;">'Flag for experimental features.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="mi" style="color: #099;">10</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="mf" style="color: #099;">0.5</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'out_prefix'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./out.CAT'</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'proteins_fasta'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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 class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'alignment_file'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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31
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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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'path_to_prodigal'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'prodigal'</span><span class="p">)</span></span>
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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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'path_to_diamond'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</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 class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_stars'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'force'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'verbose'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_log'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'help'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'IkwId'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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169
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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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170
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">specific</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND specific optional arguments'</span><span class="p">)</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_all_diamond_arguments</span><span class="p">(</span><span class="n" style="color: #333;">specific</span><span class="p">)</span></span>
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171
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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="LC172" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">'-n'</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;">'--nproc'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nproc'</span><span class="p">,</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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177
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<pre style="margin: 0;">-<span id="LC177" 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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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">(),</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" 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;">'Number of cores to deploy by DIAMOND (default: maximum).'</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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 class="s" style="color: #d14;">'--sensitive'</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 class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sensitive'</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 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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185
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<pre style="margin: 0;">-<span id="LC185" 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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186
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<pre style="margin: 0;">-<span id="LC186" 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;">'Run DIAMOND in sensitive mode (default: not enabled).'</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="s" style="color: #d14;">'--block_size'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'block_size'</span><span class="p">,</span></span>
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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;">metavar</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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191
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<pre style="margin: 0;">-<span id="LC191" 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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<td class="diff-line-num old old_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</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 class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2.0</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 class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND block-size parameter (default: 2.0). Lower numbers '</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="s" style="color: #d14;">'will decrease memory and temporary disk space usage.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">'--index_chunks'</span><span class="p">,</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" 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;">'index_chunks'</span><span class="p">,</span></span>
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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;">metavar</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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200
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<pre style="margin: 0;">-<span id="LC200" 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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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND index-chunks parameter (default: 4). Set to 1 on '</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;">'high memory machines. The parameter has no effect on '</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">'temporary disk space usage.'</span><span class="p">))</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">'--tmpdir'</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'tmpdir'</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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210
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<pre style="margin: 0;">-<span id="LC210" 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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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Directory for temporary DIAMOND files (default: directory '</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="s" style="color: #d14;">'to which output files are written).'</span><span class="p">))</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">'--compress'</span><span class="p">,</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" 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;">'compress'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC218" 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="LC219" 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="LC220" 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;">'Compress DIAMOND alignment file.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC222" class="line" lang="python"> <span class="s" style="color: #d14;">'--top'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC223" 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;">'top'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC225" 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="LC226" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">51</span><span class="p">)],</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND top parameter [0-50] (default: 50). Governs hits '</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="s" style="color: #d14;">'within range of best hit that are written to the alignment '</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="s" style="color: #d14;">'file. This is not the [-r / --range] parameter! Can only be '</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="s" style="color: #d14;">'set with the [--I_know_what_Im_doing] flag, see README.md.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">extra_args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></span>
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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 class="n" style="color: #333;">extra_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">arg</span> <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;">arg</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;">extra_args</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#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">@@ -27,9 +27,7 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">add_help</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="LC28" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">required_choice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required choice'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">required_choice</span><span class="p">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">(</span><span class="n" style="color: #333;">required</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="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">group</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="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'--fresh'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC33" 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;">'fresh'</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">@@ -44,77 +42,30 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'files that do not exist yet.'</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Optional arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">shared</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="LC46" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">'database_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;">False</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./CAT_database.{0}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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="LC50" class="line" lang="python"> <span class="n" style="color: #333;">help_</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Name of folder to which database files will be written '</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">'(default: CAT_database.{date})'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">shared</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="LC53" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./CAT_taxonomy.{0}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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="LC57" class="line" lang="python"> <span class="n" style="color: #333;">help_</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Name of folder to which taxonomy files will be downloaded '</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">'(default: CAT_taxonomy.{date})'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'path_to_diamond'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'verbose'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_log'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'help'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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47
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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="LC48" 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="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">'-d'</span><span class="p">,</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">'--database_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'database_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC53" 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="LC54" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./{0}_CAT_database'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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="LC57" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Name of folder to which database files will be written '</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">'(default: {date}_CAT_database).'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC59" 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="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">'--taxonomy_folder'</span><span class="p">,</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" 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;">'taxonomy_folder'</span><span class="p">,</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./{0}_taxonomy'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">date</span><span class="p">),</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Name of folder to which taxonomy files will be downloaded '</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">'(default: {date}_taxonomy).'</span><span class="p">))</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" 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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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_diamond'</span><span class="p">,</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" 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;">'path_to_diamond'</span><span class="p">,</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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74
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<pre style="margin: 0;">-<span id="LC74" 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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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to DIAMOND binaries. Supply if CAT prepare can not '</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">'find DIAMOND.'</span><span class="p">))</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" 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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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" 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;">'quiet'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC84" 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="LC85" 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="LC86" 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 verbosity.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC87" 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="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'verbose'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">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="LC91" 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="LC92" 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;">'Increase verbostity.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC93" 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="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_log'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC95" 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_log'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">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="LC97" 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="LC98" 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 log file.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC99" 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="LC100" class="line" lang="python"> <span class="s" style="color: #d14;">'-h'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">'--help'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC102" 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;">'help'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC103" 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;">'Show this help message and exit.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">specific</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND specific optional arguments'</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">specific</span><span class="p">,</span> <span class="s" style="color: #d14;">'nproc'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">'-n'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="s" style="color: #d14;">'--nproc'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC110" 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;">'nproc'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC112" 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="LC113" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Number of cores to deploy by DIAMOND makedb '</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">'(default: maximum).'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">extra_args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">extra_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">arg</span> <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;">arg</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;">extra_args</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#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">@@ -4,6 +4,7 @@ import argparse</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">decimal</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">multiprocessing</span></span>
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7
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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;">os</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">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">@@ -43,6 +44,404 @@ def timestamp():</td>
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<pre style="margin: 0;"> <span id="LC44" 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="LC45" class="line" lang="python"></span>
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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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help_</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'contigs_fasta'</span><span class="p">:</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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50
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<pre style="margin: 0;">+<span id="LC50" 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;">'Path to contigs fasta file.'</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</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="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">'-c'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'--contigs_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" 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;">'contigs_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'bin_fasta'</span><span class="p">:</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Path to bin fasta file.'</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">'-b'</span><span class="p">,</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">'--bin_fasta'</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" 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;">'bin_fasta'</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'bin_folder'</span><span class="p">:</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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74
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<pre style="margin: 0;">+<span id="LC74" 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;">'Path to directory containing bins.'</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">'-b'</span><span class="p">,</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">'--bin_folder'</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" 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;">'bin_folder'</span><span class="p">,</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'database_folder'</span><span class="p">:</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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86
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<pre style="margin: 0;">+<span id="LC86" 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;">'Path to folder that contains database files.'</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">'-d'</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">'--database_folder'</span><span class="p">,</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" 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;">'database_folder'</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'taxonomy_folder'</span><span class="p">:</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" 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;">'Path to folder that contains taxonomy files.'</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">'--taxonomy_folder'</span><span class="p">,</span></span>
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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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'taxonomy_folder'</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="n" style="color: #333;">metavar</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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'bin_suffix'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Suffix of bins in bin folder (default: {0}).'</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" 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;">default</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">'-s'</span><span class="p">,</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">'--bin_suffix'</span><span class="p">,</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" 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;">'bin_suffix'</span><span class="p">,</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'r'</span><span class="p">:</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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125
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<pre style="margin: 0;">+<span id="LC125" 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;">'r parameter [0-49] (default: {0:.0f}).'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">'--range'</span><span class="p">,</span></span>
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129
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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;">'r'</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;">metavar</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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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</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;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">)],</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</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="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'f'</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'f parameter [0-0.99] (default: {0:.2f}).'</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;">''</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">default</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 class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">'-f'</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="s" style="color: #d14;">'--fraction'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'f'</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;">metavar</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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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</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 class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)],</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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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;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'out_prefix'</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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154
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<pre style="margin: 0;">+<span id="LC154" 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;">'Prefix for output files (default: {0}).'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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="s" style="color: #d14;">'-o'</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 class="s" style="color: #d14;">'--out_prefix'</span><span class="p">,</span></span>
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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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'out_prefix'</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;">metavar</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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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'proteins_fasta'</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 class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Path to predicted proteins fasta file. If supplied, the '</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="s" style="color: #d14;">'protein prediction step is skipped.'</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 class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">'-p'</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="s" style="color: #d14;">'--proteins_fasta'</span><span class="p">,</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'proteins_fasta'</span><span class="p">,</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'alignment_file'</span><span class="p">:</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="s" style="color: #d14;">'Path to alignment table. If supplied, the alignment '</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="s" style="color: #d14;">'step is skipped and classification is carried out '</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="s" style="color: #d14;">'directly. A predicted proteins fasta file should also be '</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="s" style="color: #d14;">'supplied with argument [-p / --proteins].'</span><span class="p">)</span></span>
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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;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="s" style="color: #d14;">'-a'</span><span class="p">,</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="s" style="color: #d14;">'--diamond_alignment'</span><span class="p">,</span></span>
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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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'alignment_file'</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;">metavar</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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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</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 class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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 class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'path_to_prodigal'</span><span class="p">:</span></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;">if</span> <span class="n" style="color: #333;">help_</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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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Path to Prodigal binaries. Supply if CAT/BAT cannot '</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">'find Prodigal'</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_prodigal'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'path_to_prodigal'</span><span class="p">,</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;">metavar</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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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'path_to_diamond'</span><span class="p">:</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Path to DIAMOND binaries. Supply if CAT/BAT cannot find '</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="s" style="color: #d14;">'DIAMOND.'</span><span class="p">)</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_diamond'</span><span class="p">,</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" 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;">'path_to_diamond'</span><span class="p">,</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <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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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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222
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<pre style="margin: 0;">+<span id="LC222" 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 taxonomic assignments.'</span></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;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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 class="s" style="color: #d14;">'--no_stars'</span><span class="p">,</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" 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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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" 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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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <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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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
231
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<pre style="margin: 0;">+<span id="LC231" 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;">'Force overwrite existing files.'</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="s" style="color: #d14;">'--force'</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;">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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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" 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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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'quiet'</span><span class="p">:</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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240
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<pre style="margin: 0;">+<span id="LC240" 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 verbosity.'</span></span>
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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;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</span><span class="p">,</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span></span>
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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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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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;">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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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'verbose'</span><span class="p">:</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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250
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<pre style="margin: 0;">+<span id="LC250" 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;">'Increase verbosity.'</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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="s" style="color: #d14;">'--verbose'</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="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'verbose'</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;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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;">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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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no_log'</span><span class="p">:</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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259
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<pre style="margin: 0;">+<span id="LC259" 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 log file.'</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_log'</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 class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'no_log'</span><span class="p">,</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" 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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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'help'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" 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;">'Show this help message and exit.'</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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="s" style="color: #d14;">'-h'</span><span class="p">,</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="s" style="color: #d14;">'--help'</span><span class="p">,</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" 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;">'help'</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'IkwId'</span><span class="p">:</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" 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;">'Flag for experimental features.'</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="s" style="color: #d14;">'--I_know_what_Im_doing'</span><span class="p">,</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" 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;">'IkwId'</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="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
</pre>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'input_file'</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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285
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<pre style="margin: 0;">+<span id="LC285" 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;">'Path to input file.'</span></span>
</pre>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="s" style="color: #d14;">'-i'</span><span class="p">,</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="s" style="color: #d14;">'--input_file'</span><span class="p">,</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" 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;">'input_file'</span><span class="p">,</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'output_file'</span><span class="p">:</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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297
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<pre style="margin: 0;">+<span id="LC297" 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;">'Path to output file.'</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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 class="s" style="color: #d14;">'-o'</span><span class="p">,</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="s" style="color: #d14;">'--output_file'</span><span class="p">,</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" 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;">'output_file'</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;">metavar</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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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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 class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'only_official'</span><span class="p">:</span></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;">if</span> <span class="n" style="color: #333;">help_</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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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Only output official raxonomic ranks (superkingdom, '</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="s" style="color: #d14;">'phylum, class, order, family, genus, species).'</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 class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="s" style="color: #d14;">'--only_official'</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="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'only_official'</span><span class="p">,</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></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;">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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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'exclude_scores'</span><span class="p">:</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Do not include bit-score support scores in the lineage '</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="s" style="color: #d14;">'of a classification output file.'</span><span class="p">)</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="s" style="color: #d14;">'--exclude_scores'</span><span class="p">,</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" 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;">'exclude_scores'</span><span class="p">,</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" 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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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'nproc'</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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329
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<pre style="margin: 0;">+<span id="LC329" 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;">'Number of cores to deploy by DIAMOND (default: maximum).'</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="s" style="color: #d14;">'-n'</span><span class="p">,</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="s" style="color: #d14;">'--nproc'</span><span class="p">,</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" 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;">'nproc'</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="n" style="color: #333;">metavar</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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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</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 class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></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;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'sensitive'</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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341
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<pre style="margin: 0;">+<span id="LC341" 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;">'Run DIAMOND in sensitive mode (default: not enabled).'</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="s" style="color: #d14;">'--sensitive'</span><span class="p">,</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" 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;">'sensitive'</span><span class="p">,</span></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;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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 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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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'no_self_hits'</span><span class="p">:</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Do not report identical self hits by DIAMOND (default: '</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="s" style="color: #d14;">'not enabled).'</span><span class="p">)</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</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="LC353" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_self_hits'</span><span class="p">,</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" 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_self_hits'</span><span class="p">,</span></span>
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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;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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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;">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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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'block_size'</span><span class="p">:</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</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="s" style="color: #d14;">'DIAMOND block-size parameter (default: {0}). Lower '</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="s" style="color: #d14;">'numbers will decrease memory and temporary disk space '</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="s" style="color: #d14;">'usage.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">))</span></span>
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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;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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="s" style="color: #d14;">'--block_size'</span><span class="p">,</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" 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;">'block_size'</span><span class="p">,</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</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="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'index_chunks'</span><span class="p">:</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="s" style="color: #d14;">'DIAMOND index-chunks parameter (default: {0}). Set to '</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="s" style="color: #d14;">'1 on high memory machines. The parameter has no effect '</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="s" style="color: #d14;">'on temporary disk space usage.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">default</span><span class="p">))</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="s" style="color: #d14;">'--index_chunks'</span><span class="p">,</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" 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;">'index_chunks'</span><span class="p">,</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'tmpdir'</span><span class="p">:</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'Directory for temporary DIAMOND files (default: '</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="s" style="color: #d14;">'directory to which output files are written).'</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="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="s" style="color: #d14;">'--tmpdir'</span><span class="p">,</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" 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;">'tmpdir'</span><span class="p">,</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'compress'</span><span class="p">:</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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400
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<pre style="margin: 0;">+<span id="LC400" 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;">'Compress DIAMOND alignment file (default: not enabled).'</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</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="s" style="color: #d14;">'--compress'</span><span class="p">,</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" 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;">'compress'</span><span class="p">,</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</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 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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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">dest</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'top'</span><span class="p">:</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">help_</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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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">help_</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="s" style="color: #d14;">'DIAMOND top parameter [0-50] (default: {0}). Governs '</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="s" style="color: #d14;">'hits within range of best hit that are written to the '</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="s" style="color: #d14;">'alignment file. This is not the [-r / --range] '</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="s" style="color: #d14;">'parameter! Can only be set with the '</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="s" style="color: #d14;">'[--I_know_what_Im_doing] flag, see README.md.'</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" 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;">default</span><span class="p">))</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">argument_group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="s" style="color: #d14;">'--top'</span><span class="p">,</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'top'</span><span class="p">,</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">required</span><span class="p">,</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">51</span><span class="p">)],</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">,</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">help_</span><span class="p">)</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" 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="s" style="color: #d14;">'Unknown parser dest {0}.'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">dest</span><span class="p">))</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_all_diamond_arguments</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">):</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'nproc'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">())</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'sensitive'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_self_hits'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'block_size'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2.0</span><span class="p">)</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'index_chunks'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'tmpdir'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'compress'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">argument_group</span><span class="p">,</span> <span class="s" style="color: #d14;">'top'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">expand_arguments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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446
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<pre style="margin: 0;"> <span id="LC446" 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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48
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447
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<pre style="margin: 0;"> <span id="LC447" 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">@@ -55,9 +454,9 @@ def expand_arguments(args):</td>
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"></span>
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56
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'no_log'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">no_log</span><span class="p">:</span></span>
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57
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'fresh'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fresh</span><span class="p">:</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'./<span class="idiff left right">{0}.CAT_prepare</span>.fresh.log'</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;">date</span><span class="p">)</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'./<span class="idiff left right">CAT_prepare.{0}</span>.fresh.log'</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;">date</span><span class="p">)</span></span>
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59
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'fresh'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fresh</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'./<span class="idiff left right">{0}.CAT_prepare</span>.existing.log'</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;">date</span><span class="p">)</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'./<span class="idiff left right">CAT_prepare.{0}</span>.existing.log'</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;">date</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check out_prefix as the log file needs to be written to a valid</span></span>
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># location.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="245" style="width: 35px; color: rgba(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">@@ -245,21 +644,23 @@ def run_diamond(args):</td>
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644
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<pre style="margin: 0;"> <span id="LC644" 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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246
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645
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<pre style="margin: 0;"> <span id="LC645" 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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<pre style="margin: 0;"> <span id="LC646" 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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<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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<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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<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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<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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<pre style="margin: 0;">+<span id="LC647" 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: {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="LC648" 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;">no-self-hits: {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="LC649" 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: {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="LC650" 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): {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="LC651" 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: {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="LC652" 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: {8}</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="LC653" 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: {9}'</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="LC654" 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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<pre style="margin: 0;"> <span id="LC655" 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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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">top</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">no_self_hits</span><span class="p">,</span></span>
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nproc</span><span class="p">,</span></span>
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">block_size</span><span class="p">,</span></span>
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">index_chunks</span><span class="p">,</span></span>
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260
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span></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;">compression</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">top</span><span class="p">))</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">compression</span><span class="p">))</span></span>
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664
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<pre style="margin: 0;"> <span id="LC664" 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;">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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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python"></span>
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265
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666
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</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">@@ -284,6 +685,9 @@ def run_diamond(args):</td>
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sensitive</span><span class="p">:</span></span>
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686
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<pre style="margin: 0;"> <span id="LC686" 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 class="s" style="color: #d14;">'--sensitive'</span><span class="p">]</span></span>
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687
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="python"></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">no_self_hits</span><span class="p">:</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" 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 class="s" style="color: #d14;">'--no-self-hits'</span><span class="p">]</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python"></span>
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287
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691
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">)</span></span>
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288
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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289
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693
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<pre style="margin: 0;"> <span id="LC693" 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 finished abnormally.'</span></span>
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<li id="c8a6fbae43c67e6821811b75dae608fb7b1cd8d0">
<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#c8a6fbae43c67e6821811b75dae608fb7b1cd8d0"><strong>CAT_pack/single_bin.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,219 +17,32 @@ def parse_arguments():</td>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Run Bin Annotation Tool (BAT) on a single bin.'</span><span class="p">,</span></span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'CAT bin -b -d -t [options] [-h / --help]'</span><span class="p">,</span></span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">add_help</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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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> </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;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'-b'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'--bin_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" 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;">'bin_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to bin fasta file.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'-d'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'--database_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" 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;">'Path to folder that contains database files.'</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;">required</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="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'-t'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'--taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC43" 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;">'taxonomy_folder'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to folder that contains taxonomy files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'bin_fasta'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'database_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'taxonomy_folder'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Optional arguments'</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;">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="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'--range'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" 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;">'r'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC57" 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="LC58" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">)],</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">default</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="mi" style="color: #099;">5</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC62" 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;">'r parameter [0-49] (default: 5).'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC63" 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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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">'-f'</span><span class="p">,</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="s" style="color: #d14;">'--fraction'</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" 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;">'f'</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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68
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<pre style="margin: 0;">-<span id="LC68" 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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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">100</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">)],</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">DecimalAction</span><span class="p">,</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">default</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="mf" style="color: #099;">0.3</span><span class="p">),</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" 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;">'f parameter [0-0.99] (default: 0.3).'</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" 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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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="s" style="color: #d14;">'--out_prefix'</span><span class="p">,</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" 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;">'out_prefix'</span><span class="p">,</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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79
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<pre style="margin: 0;">-<span id="LC79" 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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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./out.BAT'</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">-<span id="LC83" 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;">'Prefix for output files (default: out.BAT).'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" 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="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">'-p'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'--proteins_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC87" 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;">'proteins_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC89" 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="LC90" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to predicted proteins fasta file. If supplied, BAT '</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">'will skip the protein prediction step.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC94" 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="LC95" class="line" lang="python"> <span class="s" style="color: #d14;">'-a'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">'--diamond_alignment'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC97" 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;">'alignment_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC99" 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="LC100" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to alignment table. If supplied, BAT will skip the '</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">'alignment step and directly classify the bin. A predicted '</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">'proteins fasta file should also be supplied with argument '</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">'[-p / --proteins].'</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;">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="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_prodigal'</span><span class="p">,</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'path_to_prodigal'</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="n" style="color: #333;">metavar</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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110
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<pre style="margin: 0;">-<span id="LC110" 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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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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 class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'prodigal'</span><span class="p">,</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to Prodigal binaries. Supply if BAT can not '</span></span>
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<td class="diff-line-num old old_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">'find Prodigal.'</span><span class="p">))</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" 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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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">'--path_to_diamond'</span><span class="p">,</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" 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;">'path_to_diamond'</span><span class="p">,</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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120
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<pre style="margin: 0;">-<span id="LC120" 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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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</span><span class="p">,</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to DIAMOND binaries. Supply if BAT can not find '</span></span>
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<td class="diff-line-num old old_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">'DIAMOND.'</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">-<span id="LC126" 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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<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_stars'</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="128" 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">
128
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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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129
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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="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 taxonomic assignments.'</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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<pre style="margin: 0;">-<span id="LC135" 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="LC136" 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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137
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<pre style="margin: 0;">-<span id="LC137" 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;">'Force overwrite existing files.'</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="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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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</span><span class="p">,</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;">'--quiet'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC141" 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;">'quiet'</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;">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="LC143" 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 verbosity.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC145" 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="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC147" 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;">'verbose'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC148" 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="LC149" 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="LC150" 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;">'Increase verbosity.'</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" 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="LC152" class="line" lang="python"> <span class="s" style="color: #d14;">'--no_log'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'no_log'</span><span class="p">,</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">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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155
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<pre style="margin: 0;">-<span id="LC155" 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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156
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<pre style="margin: 0;">-<span id="LC156" 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 log file.'</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 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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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="s" style="color: #d14;">'-h'</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="s" style="color: #d14;">'--help'</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'help'</span><span class="p">,</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" 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;">'Show this help message and exit.'</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" 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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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="s" style="color: #d14;">'--I_know_what_Im_doing'</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'IkwId'</span><span class="p">,</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">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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166
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<pre style="margin: 0;">-<span id="LC166" 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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167
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<pre style="margin: 0;">-<span id="LC167" 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;">'Flag for experimental features.'</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> </span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="mi" style="color: #099;">5</span><span class="p">))</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'f'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</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="mf" style="color: #099;">0.3</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'out_prefix'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'./out.BAT'</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 class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'proteins_fasta'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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31
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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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'alignment_file'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'path_to_prodigal'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'prodigal'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'path_to_diamond'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'diamond'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_stars'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'force'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'verbose'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_log'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'help'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'IkwId'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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="n" style="color: #333;">specific</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND specific optional arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">'-n'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">'--nproc'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC174" 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;">'nproc'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC176" 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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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">(),</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Number of cores to deploy by DIAMOND (default: maximum).'</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="s" style="color: #d14;">'--sensitive'</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 class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sensitive'</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 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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184
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<pre style="margin: 0;">-<span id="LC184" 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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185
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<pre style="margin: 0;">-<span id="LC185" 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;">'Run DIAMOND in sensitive mode (default: not enabled).'</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="s" style="color: #d14;">'--block_size'</span><span class="p">,</span></span>
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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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'block_size'</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;">metavar</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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190
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<pre style="margin: 0;">-<span id="LC190" 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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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">2.0</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 class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND block-size parameter (default: 2.0). Lower numbers '</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;">'will decrease memory and temporary disk space usage.'</span><span class="p">))</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="s" style="color: #d14;">'--index_chunks'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'index_chunks'</span><span class="p">,</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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199
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<pre style="margin: 0;">-<span id="LC199" 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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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND index-chunks parameter (default: 4). Set to 1 on '</span></span>
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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;">'high memory machines. The parameter has no effect on '</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;">'temporary disk space usage.'</span><span class="p">))</span></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;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</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;">'--tmpdir'</span><span class="p">,</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'tmpdir'</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">metavar</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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209
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<pre style="margin: 0;">-<span id="LC209" 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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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Directory for temporary DIAMOND files (default: directory '</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="s" style="color: #d14;">'to which output files are written).'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">specific</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="LC215" class="line" lang="python"> <span class="s" style="color: #d14;">'--compress'</span><span class="p">,</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" 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;">'compress'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC217" 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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218
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<pre style="margin: 0;">-<span id="LC218" 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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219
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<pre style="margin: 0;">-<span id="LC219" 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;">'Compress DIAMOND alignment file.'</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;">specific</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="s" style="color: #d14;">'--top'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'top'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC224" 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="LC225" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">choices</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">51</span><span class="p">)],</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'DIAMOND top parameter [0-50] (default: 50). Governs hits '</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="s" style="color: #d14;">'within range of best hit that are written to the alignment '</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="s" style="color: #d14;">'file. This is not the [-r / --range] parameter! Can only be '</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="s" style="color: #d14;">'set with the [--I_know_what_Im_doing] flag, see README.md.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_all_diamond_arguments</span><span class="p">(</span><span class="n" style="color: #333;">specific</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">extra_args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></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="n" style="color: #333;">extra_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">arg</span> <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;">arg</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;">extra_args</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#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">@@ -16,60 +16,23 @@ def parse_arguments():</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">add_help</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="LC17" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Required arguments'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'-i'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'--input_file'</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;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'input_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC25" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'input_file'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</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;">help_</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'Path to named CAT contig classification file or BAT bin '</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'classification file. Currently only official ranks are '</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'supported, and only classification files containing a single '</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'classification per contig / bin.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">required</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="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'--output_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" 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;">'output_file'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" 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;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</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;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Path to output file.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'classification per contig / bin. If you want to summarise a '</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'contig classification file, you have to supply the contigs '</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'fasta file with argument [-c / --contigs_fasta].'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="p">,</span> <span class="s" style="color: #d14;">'output_file'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></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="n" style="color: #333;">optional</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Optional arguments'</span><span class="p">)</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="LC45" 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="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">'-c'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">'--contigs_fasta'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'contigs_fasta'</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;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" 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="LC51" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">PathAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to contigs fasta file. This is required if you want '</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'to summarise a contig classification file.'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC55" 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="LC56" 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="LC57" 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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<pre style="margin: 0;">-<span id="LC58" 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="LC59" 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="LC60" 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;">'Force overwrite existing files.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC61" 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="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">'-q'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">'quiet'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC65" 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="LC66" 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="LC67" 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 verbosity.'</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;">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="LC69" class="line" lang="python"> <span class="s" style="color: #d14;">'-h'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">'--help'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC71" 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;">'help'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC72" 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;">'Show this help message and exit.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'contigs_fasta'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</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;">help_</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Path to contigs fasta file. Required if you want to '</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'summarise a contig classification file.'</span><span class="p">))</span></span>
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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;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'force'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'quiet'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">shared</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="n" style="color: #333;">optional</span><span class="p">,</span> <span class="s" style="color: #d14;">'help'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">extra_args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(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="91" style="width: 35px; color: rgba(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">@@ -128,6 +91,10 @@ def summarise_contigs(args):</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_output_file</span><span class="p">(</span></span>
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129
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <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="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="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">errors</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_in_and_output_file</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">input_file</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="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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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">True</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">errors</span><span class="p">:</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" 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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100
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<pre style="margin: 0;"> <span id="LC100" 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">@@ -323,6 +290,10 @@ def summarise_bins(args):</td>
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_output_file</span><span class="p">(</span></span>
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <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="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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292
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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;">errors</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">check</span><span class="p">.</span><span class="n" style="color: #333;">check_in_and_output_file</span><span class="p">(</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <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 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="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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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"></span>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">True</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">errors</span><span class="p">:</span></span>
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298
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<pre style="margin: 0;"> <span id="LC298" 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="LC299" class="line" lang="python"> </span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#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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2
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2
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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;">## 5.2.2</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">We have added the DIAMOND specific <span class="sb" style="color: #d14;">`--no_self_hits`</span> flag. We have also added some extra checks and removed redundancy from the parser code. Databases constructed by <span class="sb" style="color: #d14;">`CAT prepare`</span> now have a slightly different naming scheme.</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;">## 5.2.1</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">Minor bug fix for <span class="sb" style="color: #d14;">`CAT prepare`</span>.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -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_202<span class="idiff left right">01123</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_202<span class="idiff left right">10107</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_202<span class="idiff left right">01123</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown">$ tar -xvzf CAT_prepare_202<span class="idiff left right">10107</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">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 construction 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 202<span class="idiff left right">0-11-23</span>.CAT_prepare.fresh.log</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown">$ grep version 202<span class="idiff left right">1-01-07</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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<a href="https://salsa.debian.org/med-team/cat-bat/-/compare/efce185c1d7107de9f4520fb75cb670a331dee6c...6f64ab3fabc3db4355fafb5864c66ed4585a7977#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cat-bat (5.2.2-1) 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"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Mon, 18 Jan 2021 19:46:06 +0530</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">cat-bat (5.2.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version</span>
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