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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ariba">Debian Med / ariba</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9">0c1eaaa8</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-05-15T17:03:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.12.0+ds</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#4686ec029c747c4997c3461db20e52276dfa268d">
ariba/assembly.py
</a>
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<li class="file-stats">
<a href="#aa7da031b0960d2609000e527dd7639d1640ae89">
ariba/cdhit.py
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<li class="file-stats">
<a href="#9feea2d377e2ad6ec437b52ed355c2ba7aa4b024">
ariba/cluster.py
</a>
</li>
<li class="file-stats">
<a href="#680709b3fecae42947961f03844603f4aa5838d9">
ariba/external_progs.py
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</li>
<li class="file-stats">
<a href="#58054356e11f7717cfa55a32bab7ebacb60c77c4">
ariba/read_filter.py
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<li class="file-stats">
<a href="#acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4">
ariba/ref_genes_getter.py
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<li class="file-stats">
<a href="#c5ffa08f04d46472e2c42797aeac5116772620fc">
ariba/tasks/prepareref.py
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<li class="file-stats">
<a href="#c1cda3d4fe208ef7cf9d021c40f13508564fa3c6">
ariba/tasks/run.py
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<li class="file-stats">
<a href="#d08f397161ea3da6f6624940aa4dfb27366c73d7">
ariba/tests/assembly_test.py
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<li class="file-stats">
<a href="#01d994c007903fa3e0dfce7bf9f68109c0fc5866">
<span class="new-file">
+
ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa
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<li class="file-stats">
<a href="#35ebe92a3edefee20deffeb3c5cc6fa48baaed09">
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+
ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa
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<li class="file-stats">
<a href="#48d9f73ceff4f161a3d7804763050e91a4630e78">
<span class="new-file">
+
ariba/tests/ref_genes_getter_test.py
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<li class="file-stats">
<a href="#efbed21719f79b94d7668d1e8501575596560855">
ariba/versions.py
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<li class="file-stats">
<a href="#be7d3d236cd32b79a1fb8d70218ac327107688bb">
scripts/ariba
</a>
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
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</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Antimicrobial Resistance Identification By Assembly</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">For how to use ARIBA, please see the <span class="p">[</span><span class="nv" style="color: teal;">ARIBA wiki page</span><span class="p">][</span><span class="ss" style="color: #990073;">ARIBA wiki</span><span class="p">]</span>.</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/ariba.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/ariba)</span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg</span><span class="p">)</span>](https://github.com/s<span class="idiff left right">sjunnebo</span>/ariba/blob/master/LICENSE)</span>
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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg</span><span class="p">)</span>](https://github.com/s<span class="idiff left right">anger-pathogens</span>/ariba/blob/master/LICENSE)</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000131-brightgreen.svg</span><span class="p">)</span>](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000131)</span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contents</span></span>
</pre>
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<br>
</li>
<li id="4686ec029c747c4997c3461db20e52276dfa268d">
<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#4686ec029c747c4997c3461db20e52276dfa268d"><strong>ariba/assembly.py</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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">@@ -59,7 +59,7 @@ class Assembly:</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threads</span></span>
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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extern_progs</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 old old_line" data-linenumber="62" 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="LC62" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">()</span></span>
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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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">
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assembler</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'spades'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extern_progs</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#aa7da031b0960d2609000e527dd7639d1640ae89"><strong>ariba/cdhit.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">@@ -27,7 +27,7 @@ class Runner:</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length_diff_cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length_diff_cutoff</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">verbose</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_cluster_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_cluster_number</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;">fail_on_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="LC30" class="line" lang="python"> <span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;">fail_on_error</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cd_hit_est</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extern_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exe</span><span class="p">(</span><span class="s" style="color: #d14;">'cdhit'</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>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#9feea2d377e2ad6ec437b52ed355c2ba7aa4b024"><strong>ariba/cluster.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">@@ -130,7 +130,7 @@ class Cluster:</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extern_progs</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="LC133" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assembler</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'spades'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extern_progs</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#680709b3fecae42947961f03844603f4aa5838d9"><strong>ariba/external_progs.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">@@ -20,10 +20,19 @@ prog_to_default = {</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="n" style="color: #333;">prog_to_env_var</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="s" style="color: #d14;">'ARIBA_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">prog_to_default</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">{</span><span class="s" style="color: #d14;">'nucmer'</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>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Nucmer 3.1 'nucmer --version' outputs this:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># nucmer</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># NUCmer (NUCleotide MUMmer) version 3.1</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Numcer 4 'nucmer --version' outputs this:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># 4.0.0beta2</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># ... make the regex permissive and hope things</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># still work for later versions</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">prog_to_version_cmd</span> <span class="o" style="font-weight: 600;">=</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;">'bowtie2'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'.*bowtie2.*version (.*)$'</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;">'cdhit'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'CD-HIT version ([0-9</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">.]+) </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</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="s" style="color: #d14;">'nucmer'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left">^NUCmer </span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s" style="color: #d14;"><span class="idiff">(NUCleotide MUMmer</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s" style="color: #d14;"><span class="idiff">) version ([0-9</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s" style="color: #d14;"><span class="idiff right">.]+</span>)'</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;">'nucmer'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left">([0-9]+</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s" style="color: #d14;"><span class="idiff">.[0-9</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s" style="color: #d14;"><span class="idiff right">.]+.*$</span>)'</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">'spades'</span><span class="p">:</span> <span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'SPAdes</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+v([0-9</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,11 +49,12 @@ prog_optional = set([</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ExternalProgs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">fail_on_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="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">fail_on_error</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_report</span> <span class="o" style="font-weight: 600;">=</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;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_deps_ok</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="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">versions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">using_spades</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">using_spades</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose</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;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'{:_^79}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="s" style="color: #d14;">' Checking dependencies and their versions '</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">@@ -53,6 +63,9 @@ class ExternalProgs:</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">prog</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">prog_to_default</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'spades'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">using_spades</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></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;">msg_sink</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">errors</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prog</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">prog_optional</span><span class="p">:</span></span>
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58
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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;">msg_sink</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">warnings</span></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#58054356e11f7717cfa55a32bab7ebacb60c77c4"><strong>ariba/read_filter.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,7 @@ class ReadFilter:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_fh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_fh</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extern_progs</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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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extern_progs</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4"><strong>ariba/ref_genes_getter.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">@@ -7,6 +7,8 @@ import tarfile</td>
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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;">pyfastaq</span></span>
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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;">time</span></span>
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9
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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;">json</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;">subprocess</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" 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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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ariba</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">common</span><span class="p">,</span> <span class="n" style="color: #333;">card_record</span><span class="p">,</span> <span class="n" style="color: #333;">vfdb_parser</span><span class="p">,</span> <span class="n" style="color: #333;">megares_data_finder</span><span class="p">,</span> <span class="n" style="color: #333;">megares_zip_parser</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -186,6 +188,19 @@ class RefGenesGetter:</td>
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'and in your methods say that version'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">'of the database was used'</span><span class="p">)</span></span>
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187
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"></span>
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188
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_genetic_epi_database_from_bitbucket</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">db_name</span><span class="p">,</span> <span class="n" style="color: #333;">outdir</span><span class="p">,</span> <span class="n" style="color: #333;">git_commit</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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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">{</span><span class="s" style="color: #d14;">'plasmidfinder'</span><span class="p">,</span> <span class="s" style="color: #d14;">'resfinder'</span><span class="p">,</span> <span class="s" style="color: #d14;">'virulence_finder'</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;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'git clone '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'https://bitbucket.org/genomicepidemiology/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">db_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_db.git '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">outdir</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;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">git_commit</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="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;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'cd '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' && git checkout '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">git_commit</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>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Using this git commit for '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">db_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' database:'</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;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">'cd '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' && git log -n 1'</span><span class="p">,</span> <span class="n" style="color: #333;">shell</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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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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189
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_from_resfinder</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outprefix</span><span class="p">):</span></span>
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190
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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;">outprefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">outprefix</span><span class="p">)</span></span>
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191
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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;">final_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.fa'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="208" style="width: 35px; color: rgba(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">@@ -193,17 +208,22 @@ class RefGenesGetter:</td>
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193
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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;">tmpdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tmp.download'</span></span>
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194
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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;">current_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>
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195
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</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="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'old'</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="k" style="font-weight: 600;">try</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</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="k" style="font-weight: 600;">except</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="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error mkdir/chdir '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpdir</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>
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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;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'resfinder.zip'</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;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'curl -X POST --data "folder=resfinder&filename=resfinder.zip" -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' https://cge.cbs.dtu.dk/cge/download_data.php'</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;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Downloading data with:'</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'unzip '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span><span class="p">)</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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="n" style="color: #333;">RefGenesGetter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_genetic_epi_database_from_bitbucket</span><span class="p">(</span><span class="s" style="color: #d14;">'resfinder'</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">git_commit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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198
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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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
</pre>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error mkdir/chdir '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'resfinder.zip'</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'curl -X POST --data "folder=resfinder&filename=resfinder.zip" -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' https://cge.cbs.dtu.dk/cge/download_data.php'</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Downloading data with:'</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'unzip '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Combining downloaded fasta files...'</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;">fout_fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pyfastaq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">open_file_write</span><span class="p">(</span><span class="n" style="color: #333;">final_fasta</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">@@ -222,7 +242,7 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC243" 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;">'.'</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="LC225" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>names are not unique across the files</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span>names are not unique across the files</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">used_names</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">used_names</span><span class="p">[</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">used_names</span><span class="p">[</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">])</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="310" style="width: 35px; color: rgba(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="330" style="width: 35px; color: rgba(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">@@ -310,17 +330,21 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">tmpdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tmp.download'</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">current_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'old'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error mkdir/chdir '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpdir</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>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'plasmidfinder.zip'</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;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'curl -X POST --data "folder=plasmidfinder&filename=plasmidfinder.zip" -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' https://cge.cbs.dtu.dk/cge/download_data.php'</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Downloading data with:'</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</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;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'unzip '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</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="k" style="font-weight: 600;">else</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;">RefGenesGetter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_genetic_epi_database_from_bitbucket</span><span class="p">(</span><span class="s" style="color: #d14;">'plasmidfinder'</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">git_commit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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315
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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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</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="k" style="font-weight: 600;">except</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;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error mkdir/chdir '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpdir</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>
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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;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'plasmidfinder.zip'</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'curl -X POST --data "folder=plasmidfinder&filename=plasmidfinder.zip" -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' https://cge.cbs.dtu.dk/cge/download_data.php'</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Downloading data with:'</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'unzip '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</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>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Combining downloaded fasta files...'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">fout_fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pyfastaq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">open_file_write</span><span class="p">(</span><span class="n" style="color: #333;">final_fasta</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">@@ -357,8 +381,13 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_from_srst2_argannot</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outprefix</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;">srst2_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.2.0'</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">srst2_url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'https://github.com/katholt/srst2/raw/v'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">srst2_version</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/data/ARGannot.r1.fasta'</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</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="LC385" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'r2'</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">{</span><span class="s" style="color: #d14;">'r1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'r2'</span><span class="p">}:</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'srst2_argannot version must be r1 or r2. Got this: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</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>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">version_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.r1'</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'r1'</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'_r2'</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;">srst2_url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'https://raw.githubusercontent.com/katholt/srst2/master/data/ARGannot'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">version_string</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.fasta'</span></span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">srst2_fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.original.fa'</span></span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'wget -O '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">srst2_fa</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">srst2_url</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">command</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -389,7 +418,9 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'If you use this downloaded data, please cite:'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'"SRST2: Rapid genomic surveillance for public health and hospital microbiology labs",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Inouye et al 2014, Genome Medicine, PMID: 25422674</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">argannot_ref</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'and in your methods say that the ARG-ANNOT sequences were used from version'</span><span class="p">,</span> <span class="n" style="color: #333;">srst2_version</span><span class="p">,</span> <span class="s" style="color: #d14;">'of SRST2.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Use to also output the version of SRST2 here, but the r2 version of their</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># fasta file was made after SRST2 release 0.2.0. At the time of writing this,</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># 0.2.0 is the latest release, ie r2 isn't in an SRST2 release.</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_from_vfdb_core</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outprefix</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">@@ -427,6 +458,31 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'"VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on",</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Chen LH et al 2016, Nucleic Acids Res. 44(Database issue):D694-D697. PMID: 26578559</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_fix_virulencefinder_fasta_file</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="s" style="color: #d14;">'''Some line breaks are missing in the FASTA files from</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"><span class="s" style="color: #d14;"> viruslence finder. Which means there are lines like this:</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"><span class="s" style="color: #d14;"> AAGATCCAATAACTGAAGATGTTGAACAAACAATTCATAATATTTATGGTCAATATGCTATTTTCGTTGA</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"><span class="s" style="color: #d14;"> AGGTGTTGCGCATTTACCTGGACATCTCTCTCCATTATTAAAAAAATTACTACTTAAATCTTTATAA>coa:1:BA000018.3</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"><span class="s" style="color: #d14;"> ATGAAAAAGCAAATAATTTCGCTAGGCGCATTAGCAGTTGCATCTAGCTTATTTACATGGGATAACAAAG</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"><span class="s" style="color: #d14;"> and therefore the sequences are messed up when we parse them. Also</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"><span class="s" style="color: #d14;"> one has a > at the end, then the seq name on the next line.</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"><span class="s" style="color: #d14;"> This function fixes the file by adding line breaks'''</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f_in</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f_out</span><span class="p">:</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f_in</span><span class="p">:</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'>'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">):</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'WARNING: found line with ">" at the end! Fixing. Line:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' in file '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'WARNING: found line with ">" not at the start! Fixing. Line:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' in file '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">line1</span><span class="p">,</span> <span class="n" style="color: #333;">line2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">)</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="n" style="color: #333;">line2</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_from_virulencefinder</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outprefix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">outprefix</span><span class="p">)</span></span>
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="n" style="color: #333;">final_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.fa'</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">@@ -434,17 +490,21 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"> <span class="n" style="color: #333;">tmpdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tmp.download'</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">current_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">()</span></span>
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'old'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error mkdir/chdir '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'plasmidfinder.zip'</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'curl -X POST --data "folder=virulencefinder&filename=virulencefinder.zip" -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' https://cge.cbs.dtu.dk/cge/download_data.php'</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Downloading data with:'</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'unzip '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span><span class="p">)</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">RefGenesGetter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_genetic_epi_database_from_bitbucket</span><span class="p">(</span><span class="s" style="color: #d14;">'plasmidfinder'</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">git_commit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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439
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error mkdir/chdir '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"></span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'plasmidfinder.zip'</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'curl -X POST --data "folder=virulencefinder&filename=virulencefinder.zip" -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' https://cge.cbs.dtu.dk/cge/download_data.php'</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Downloading data with:'</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'unzip '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span><span class="p">)</span></span>
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"></span>
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Combining downloaded fasta files...'</span><span class="p">)</span></span>
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">fout_fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pyfastaq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">open_file_write</span><span class="p">(</span><span class="n" style="color: #333;">final_fasta</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="454" style="width: 35px; color: rgba(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="514" style="width: 35px; color: rgba(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">@@ -454,7 +514,9 @@ class RefGenesGetter:</td>
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454
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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455
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515
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.fsa'</span><span class="p">):</span></span>
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456
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">file_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pyfastaq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_reader</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">fix_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.fix.fsa'</span><span class="p">)</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">RefGenesGetter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_fix_virulencefinder_fasta_file</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">),</span> <span class="n" style="color: #333;">fix_file</span><span class="p">)</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="n" style="color: #333;">file_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pyfastaq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_reader</span><span class="p">(</span><span class="n" style="color: #333;">fix_file</span><span class="p">)</span></span>
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458
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">file_reader</span><span class="p">:</span></span>
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459
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">original_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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460
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522
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#c5ffa08f04d46472e2c42797aeac5116772620fc"><strong>ariba/tasks/prepareref.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,7 @@ def run(options):</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">no_cdhit</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cdhit_clusters</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">'Cannot use both --no_cdhit and --cdhit_clusters. Neither or exactly one of those options must be used'</span><span class="p">)</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">extern_progs</span><span class="p">,</span> <span class="n" style="color: #333;">version_report_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_all_versions</span><span class="p">()</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">extern_progs</span><span class="p">,</span> <span class="n" style="color: #333;">version_report_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_all_versions</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">version_report_lines</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#c1cda3d4fe208ef7cf9d021c40f13508564fa3c6"><strong>ariba/tasks/run.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">@@ -35,7 +35,7 @@ def run(options):</td>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Output directory already exists. ARIBA makes the output directory. Cannot continue.'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</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;">sys</span><span class="o" style="font-weight: 600;">.</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="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">extern_progs</span><span class="p">,</span> <span class="n" style="color: #333;">version_report_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ariba</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_all_versions</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;">extern_progs</span><span class="p">,</span> <span class="n" style="color: #333;">version_report_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ariba</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_all_versions</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">assembler</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'spades'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">version_report_lines</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#d08f397161ea3da6f6624940aa4dfb27366c73d7"><strong>ariba/tests/assembly_test.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">@@ -9,7 +9,7 @@ from ariba import external_progs</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">modules_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">assembly</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">data_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">modules_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'tests'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestAssembly</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_run_fermilite</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#01d994c007903fa3e0dfce7bf9f68109c0fc5866"><strong>ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>seq1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ACGT</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">A</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">>seq2</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AGT</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">AC>seq3</span>
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7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ACGT</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">>seq4</span>
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9
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">AACGT></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">seq5</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">AAC</span></pre>
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<li id="35ebe92a3edefee20deffeb3c5cc6fa48baaed09">
<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#35ebe92a3edefee20deffeb3c5cc6fa48baaed09"><strong>ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>seq1</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ACGT</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">A</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">>seq2</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AGT</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">AC</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">>seq3</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ACGT</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">>seq4</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">AACGT</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">>seq5</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">AAC</span></pre>
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<li id="48d9f73ceff4f161a3d7804763050e91a4630e78">
<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#48d9f73ceff4f161a3d7804763050e91a4630e78"><strong>ariba/tests/ref_genes_getter_test.py</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">filecmp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">ariba</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ref_genes_getter</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">modules_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">ref_genes_getter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">data_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">modules_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'tests'</span><span class="p">,</span> <span class="s" style="color: #d14;">'data'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestRefGenesGetter</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fix_virulencefinder_fasta_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">'''test _fix_virulencefinder_fasta_file'''</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">infile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref_genes_getter.fix_virulencefinder_fasta_file.in.fa'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">tmp_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'tmp.test.ref_genes_getter.fix_virulencefinder_fasta_file.out.fa'</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">expected_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'ref_genes_getter.fix_virulencefinder_fasta_file.out.fa'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">ref_genes_getter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">RefGenesGetter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_fix_virulencefinder_fasta_file</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">filecmp</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">cmp</span><span class="p">(</span><span class="n" style="color: #333;">expected_file</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="n" style="color: #333;">shallow</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 class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#efbed21719f79b94d7668d1e8501575596560855"><strong>ariba/versions.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">@@ -17,8 +17,8 @@ package_max_versions = {</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><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>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_all_versions</span><span class="p">(</span><span class="n" style="color: #333;">raise_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="LC21" class="line" lang="python"> <span class="n" style="color: #333;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;">fail_on_error</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_all_versions</span><span class="p">(</span><span class="n" style="color: #333;">raise_error</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></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;">extern_progs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">external_progs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ExternalProgs</span><span class="p">(</span><span class="n" style="color: #333;">fail_on_error</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">using_spades</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">using_spades</span></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;">report_lines</span> <span class="o" style="font-weight: 600;">=</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;">'ARIBA version: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ariba_version</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#be7d3d236cd32b79a1fb8d70218ac327107688bb"><strong>scripts/ariba</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">@@ -62,7 +62,7 @@ subparser_getref = subparsers.add_parser(</td>
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<pre style="margin: 0;"> <span id="LC62" 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;">'Download reference data from one of a few supported public resources'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"><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;">subparser_getref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--debug'</span><span class="p">,</span> <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 class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Do not delete temporary downloaded files'</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;">subparser_getref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Version of reference data to download. If not used, gets the latest version. <span class="idiff left right">Only applies to card and megares</span>'</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;">subparser_getref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Version of reference data to download. If not used, gets the latest version. <span class="idiff left right">Applies to: card, megares, plasmidfinder, resfinder, srst2_argannot, virulencefinder. For plasmid/res/virulencefinder: default is to get latest from bitbucket - supply git commit hash to get a specific version from bitbucket, or use "old " to get from old website. For srst2_argannot: default is latest version r2, use r1 to get the older version</span>'</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;">subparser_getref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'db'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Database to download. Must be one of: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">allowed_dbs</span><span class="p">),</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">allowed_dbs</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"DB name"</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;">subparser_getref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'outprefix'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Prefix of output filenames'</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;">subparser_getref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ariba</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tasks</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/ariba/commit/0c1eaaa8e446b066e05d707a211cba03ab8474c9#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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">@@ -55,7 +55,7 @@ vcfcall_mod = Extension(</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">setup</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;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">minimap_mod</span><span class="p">,</span> <span class="n" style="color: #333;">fermilite_mod</span><span class="p">,</span> <span class="n" style="color: #333;">vcfcall_mod</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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ariba'</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;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.1<span class="idiff left right">1.1</span>'</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;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.1<span class="idiff left right">2.0</span>'</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;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ARIBA: Antibiotic Resistance Identification By Assembly'</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;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</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;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'test_run_data/*'</span><span class="p">]},</span></span>
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