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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/plasmidid">Debian Med / plasmidid</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plasmidid/-/commit/14fc856f1e788a910ed2e01e7fc61bd0a313c3a2">14fc856f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-06-26T17:53:41+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.6.3+dfsg</pre>
</li>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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</li>
<li class="file-stats">
<a href="#5013f78c1a777b3328f8fd9f2b51313d209f022c">
bin/download_plasmid_database.py
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<li class="file-stats">
<a href="#8a077ed81785711c0820fbc816c88718ecc7259e">
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+
bin/mashclust.py
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<li class="file-stats">
<a href="#aa410d7cdf4c86039dd72deb31e6663794fe88a5">
bin/spades_assembly.sh
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<li class="file-stats">
<a href="#b19e0dcc2ca89f499c5c1830732036c0a3f93743">
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+
bin/summary_report_pid.py
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<li class="file-stats">
<a href="#14a323f407938be84e97642eeb9f07cc91aa822e">
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+
databases/card.fasta
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<li class="file-stats">
<a href="#6a8c79ed11367ec6386c5fdc2a70426232e381cd">
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+
img/pipeline_pID.png
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</li>
<li class="file-stats">
<a href="#c2708568ecdb3663570cb2c22e36227c1ce85631">
plasmidID
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</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/plasmidid/-/commit/14fc856f1e788a910ed2e01e7fc61bd0a313c3a2#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![CircleCI Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://circleci.com/gh/circleci/circleci-docs.svg?style=shield</span><span class="p">)</span>](https://circleci.com/gh/BU-ISCIII/plasmidID) <span class="p">[</span><span class="nv" style="color: #008080;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-blue.svg</span><span class="p">)</span>](https://www.gnu.org/licenses/gpl-3.0) <span class="p">[</span><span class="nv" style="color: #008080;">![CircleCi Community</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/community-CircleCI%20Discuss-343434.svg</span><span class="p">)</span>](https://discuss.circleci.com) <span class="p">[</span><span class="nv" style="color: #008080;">![Scif</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/Filesystem-Scientific-brightgreen.svg</span><span class="p">)</span>](https://sci-f.github.io)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/fusion-report/README.html)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![CircleCI Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://circleci.com/gh/circleci/circleci-docs.svg?style=shield</span><span class="p">)</span>](https://circleci.com/gh/BU-ISCIII/plasmidID) <span class="p">[</span><span class="nv" style="color: #008080;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-blue.svg</span><span class="p">)</span>](https://www.gnu.org/licenses/gpl-3.0) <span class="p">[</span><span class="nv" style="color: #008080;">![Scif</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/Filesystem-Scientific-brightgreen.svg</span><span class="p">)</span>](https://sci-f.github.io)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;"># plasmidID <img align="left" src="https://github.com/BU-ISCIII/plasmidID/blob/develop/img/plasmidID_logo.png" alt="Logo" width="100"></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line old" data-linenumber="10" 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="LC9" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">#f03c15</span><span class="p">](</span><span class="sx" style="color: #d14;">https://placehold.it/15/f03c15/000000?text=+</span><span class="p">)</span> <span class="gs" style="font-weight: 600;">**PlasmidID is already available to download**</span> !<span class="p">[</span><span class="nv" style="color: #008080;">#f03c15</span><span class="p">](</span><span class="sx" style="color: #d14;">https://placehold.it/15/f03c15/000000?text=+</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Introduction</span><span class="p">](</span><span class="sx" style="color: #d14;">#introduction</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Requirements</span><span class="p">](</span><span class="sx" style="color: #d14;">#requirements</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Software</span><span class="p">](</span><span class="sx" style="color: #d14;">#software</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Plasmid database</span><span class="p">](</span><span class="sx" style="color: #d14;">#plasmid-database</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Install from source</span><span class="p">](</span><span class="sx" style="color: #d14;">#install-from-source</span><span class="p">)</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Install using conda</span><span class="p">](</span><span class="sx" style="color: #d14;">#install-using-conda</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Quick usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#quick-usage</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#usage</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Output</span><span class="p">](</span><span class="sx" style="color: #d14;">#output</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Annotation file</span><span class="p">](</span><span class="sx" style="color: #d14;">#annotation-file</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Illustrated pipeline</span><span class="p">](</span><span class="sx" style="color: #d14;">#illustrated-pipeline</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Docker</span><span class="p">](</span><span class="sx" style="color: #d14;">#docker</span><span class="p">)</span></span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Introduction</span></span>
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10
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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11
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown">PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.</span>
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12
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
</pre>
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13
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<td class="diff-line-num new_line old" data-linenumber="28" 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="LC13" class="line" lang="markdown">PlasmidID is a <span class="gs" style="font-weight: 600;">**computational pipeline**</span> implemented in <span class="gs" style="font-weight: 600;">**BASH**</span> that maps Illumina reads over plasmid database sequences. The most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a <span class="gs" style="font-weight: 600;">**circular image**</span> which allow user to determine plasmidic composition in any bacterial sample.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">PlasmidID is a <span class="gs" style="font-weight: 600;">**computational pipeline**</span> implemented in <span class="gs" style="font-weight: 600;">**BASH**</span> that maps Illumina reads over plasmid database sequences. The k-mer filtered, most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a <span class="gs" style="font-weight: 600;">**circular image**</span> which allow user to determine plasmidic composition in any bacterial sample.</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Requirements</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Software</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Python >=3.6</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.python.org/</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Trimmomatic v0.33</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.usadellab.org/cms/?page=trimmomatic</span><span class="p">)(</span><span class="sx" style="color: #d14;">Optional</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Spades v3.8</span><span class="p">](</span><span class="sx" style="color: #d14;">http://cab.spbu.ru/software/spades/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">Optional</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Perl v5.26.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.perl.org/get.html</span><span class="p">)</span></span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">NCBI_blast + v2.2.3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download</span><span class="p">)</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Bedtools v2.25</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bedtools.readthedocs.io/en/latest/</span><span class="p">)</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Bowtie 2 v2.2.4</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bowtie-bio.sourceforge.net/bowtie2/index.shtml</span><span class="p">)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">SAMtools v1.2</span><span class="p">](</span><span class="sx" style="color: #d14;">http://samtools.sourceforge.net/</span><span class="p">)</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">prokka v1.12</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.vicbioinformatics.com/software.prokka.shtml</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">cd-hit v4.6.6</span><span class="p">](</span><span class="sx" style="color: #d14;">http://weizhongli-lab.org/cd-hit/</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">no</span> longer needed since v1.6)</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">circos v0.69.3</span><span class="p">](</span><span class="sx" style="color: #d14;">http://circos.ca/software/download/circos/</span><span class="p">)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">mash v2.2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/marbl/Mash</span><span class="p">)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Plasmid database</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">Since version v1.5.1 plasmid database can be downloaded with the following command:</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="p">```</span><span class="nl">Bash</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;"> download_plasmid_database.py -o FOLDER</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p">```</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Install from source</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">Install all dependencies and add them to $PATH</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown">git clone https://github.com/BU-ISCIII/plasmidID.git</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown">Add plasmidID and ./bin to $PATH</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Install using conda</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown">This option is recomended.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown">Install <span class="p">[</span><span class="nv" style="color: #008080;">Anaconda3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.anaconda.com/distribution/</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="p">```</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown">conda install -c conda-forge -c bioconda plasmidid</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="p">```</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown">Wait for the environment to solve</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown">Ignore warnings/errors</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Quick usage</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"></span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown">Illumina paired-end</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="p">```</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown">plasmidID \</span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown">-1 SAMPLE_R1.fastq.gz \</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown">-2 SAMPLE_R2.fastq.gz \</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown">-d YYYY-MM-DD_plasmids.fasta \</span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown">-c SAMPLE_assembled_contigs.fasta \</span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown">--no-trim \</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown">-s SAMPLE</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="p">```</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">SMRT sequencing (only contigs)</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="p">```</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown">plasmidID \</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">-d YYYY-MM-DD_plasmids.fasta \</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown">-c SAMPLE_contigs.fasta \</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown">-s SAMPLE</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="p">```</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown">Annotate any fasta you want</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="p">```</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown">plasmidID \</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">-d YYYY-MM-DD_plasmids.fasta \</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown">-c SAMPLE_assembled_contigs.fasta \</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown">-a annotation_file \</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown">-s SAMPLE</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown">More info about <span class="p">[</span><span class="nv" style="color: #008080;">annotation file</span><span class="p">](</span><span class="sx" style="color: #d14;">#annotation-file</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown">If there are several samples in the same GROUP folder</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown">summary_report_pid.py -i NO_GROUP/</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="p">```</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown">usage : plasmidID <-1 R1> <-2 R2> <-d database(fasta)> <-s sample_name> [-g group_name] [options]</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"> Mandatory input data:</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"> -1 | --R1 <filename> reads corresponding to paired-end R1 (mandatory)</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"> -2 | --R2 <filename> reads corresponding to paired-end R2 (mandatory)</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"> -d | --database <filename> database to map and reconstruct (mandatory)</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"> -s | --sample <string> sample name (mandatory), less than 37 characters</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"> Optional input data:</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"> -g | --group <string> group name (optional). If unset, samples will be gathered in NO_GROUP group</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"> -c | --contigs <filename> file with contigs. If supplied, plasmidID will not assembly reads</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"> -a | --annotate <filename> file with configuration file for specific annotation</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"> -o <output_dir> output directory, by default is the current directory</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"> Pipeline options:</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"> --explore Relaxes default parameters to find less reliable relationships within data supplied and database</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"> --only-reconstruct Database supplied will not be filtered and all sequences will be used as scaffold</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"> This option does not require R1 and R2, instead a contig file can be supplied</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"> -w Undo winner takes it all algorithm when clustering by kmer - QUICKER MODE</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"> Trimming:</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"> --trimmomatic-directory Indicate directory holding trimmomatic .jar executable</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"> --no-trim Reads supplied will not be quality trimmed</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"> Coverage and Clustering:</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown"> -C | --coverage-cutoff <int> minimun coverage percentage to select a plasmid as scafold (0-100), default 80</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"> -S | --coverage-summary <int> minimun coverage percentage to include plasmids in summary image (0-100), default 90</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"> -f | --cluster <int> kmer identity to cluster plasmids into the same representative sequence (0 means identical) (0-1), default 0.5</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"> -k | --kmer <int> identity to filter plasmids from the database with kmer approach (0-1), default 0.95</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"> Contig local alignment</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"> -i | --alignment-identity <int> minimun identity percentage aligned for a contig to annotate, default 90</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"> -l | --alignment-percentage <int> minimun length percentage aligned for a contig to annotate, default 20</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"> -L | --length-total <int> minimun alignment length to filter blast analysis</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"> --extend-annotation <int> look for annotation over regions with no homology found (base pairs), default 500bp</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"> Draw images:</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"> --config-directory <dir> directory holding config files, default config_files/</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"> --config-file-individual <file-name> file name of the individual file used to reconstruct</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"> Additional options:</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"> -M | --memory <int> max memory allowed to use</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"> -T | --threads <int> number of threads</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"> -v | --version version</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"> -h | --help display usage message</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown">example: ./plasmidID.sh -1 ecoli_R1.fastq.gz -2 ecoli_R2.fastq.gz -d database.fasta -s ECO_553 -G ENTERO</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"> ./plasmidID.sh -1 ecoli_R1.fastq.gz -2 ecoli_R2.fastq.gz -d PacBio_sample.fasta -c scaffolds.fasta -C 60 -s ECO_60 -G ENTERO --no-trim</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Examples</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"></span>
</pre>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown">Under construction</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"></span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Output</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"></span>
</pre>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown">Since v1.6, the more relevant output is located in GROUP/SAMPLE folder:</span>
</pre>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"></span>
</pre>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"><span class="p">-</span> <span class="gs" style="font-weight: 600;">**SAMPLE_final_results.html(.tab)**</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"><span class="p"> -</span> id: Name of the accession number of reference</span>
</pre>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"><span class="p"> -</span> length: length of the reference sequence</span>
</pre>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"><span class="p"> -</span> species: species of the reference sequence</span>
</pre>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"><span class="p"> -</span> description: rest of reference fasta header</span>
</pre>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"><span class="p"> -</span> contig_name: number of the contigs that align the minimun required for complete contig track</span>
</pre>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"><span class="p"> -</span> SAMPLE:</span>
</pre>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="markdown"><span class="p"> -</span> Image of the reconstructed plasmid (click to open in new tab)</span>
</pre>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="markdown"><span class="p"> -</span> MAPPING % (percentage): percentage of reference covered with reads</span>
</pre>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"><span class="p"> -</span> X for contig mode (gray colour)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="markdown"><span class="p"> -</span> Orientative colouring (the closer to 100% the better)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"><span class="p"> -</span> ALIGN FR (fraction_covered): total length of contigs aligned (complete) / reference sequence length</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"><span class="p"> -</span> Orientative colouring (the closer to 1 the better)</span>
</pre>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"> </span>
</pre>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"></span>
</pre>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Annotation file</span></span>
</pre>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown">Under construction</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Illustrated pipeline</span></span>
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14
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown"></span>
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15
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown">This image sumarizes PlasmidID pipeline, including the most important steps.</span>
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16
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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="markdown">For furder details, including:</span>
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17
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<td class="diff-line-num new_line old" data-linenumber="196" 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="LC17" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Database download</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/BU-ISCIII/plasmidID/wiki/Plasmid-Database</span><span class="p">)</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Dependencies</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/BU-ISCIII/plasmidID/wiki/Installation-and-Dependencies</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<td class="diff-line-num new_line old" data-linenumber="196" 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="LC19" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Execution</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/BU-ISCIII/plasmidID/wiki/Execution</span><span class="p">)</span></span>
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20
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<td class="diff-line-num new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">Results interpretation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/BU-ISCIII/plasmidID/wiki/Understanding-the-image:-track-by-track</span><span class="p">)</span></span>
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21
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<td class="diff-line-num new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown"><span class="p">-</span> and more, please visit: <span class="p">[</span><span class="nv" style="color: #008080;">**PLASMIDID WIKI**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/BU-ISCIII/plasmidID/wiki</span><span class="p">)</span></span>
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22
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="markdown"></span>
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23
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<td class="diff-line-num new_line old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">align=</span><span class="s" style="color: #d14;">"center"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://github.com/BU-ISCIII/plasmidID/blob/master/img/Short_pipeline.png"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"workflow_small"</span> <span class="na" style="color: #008080;">width=</span><span class="s" style="color: #d14;">"500"</span><span class="nt" style="color: #000080;">></span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"><span class="nt" style="color: #000080;"><p</span> <span class="na" style="color: #008080;">align=</span><span class="s" style="color: #d14;">"center"</span><span class="nt" style="color: #000080;">><img</span> <span class="na" style="color: #008080;">src=</span><span class="s" style="color: #d14;">"https://github.com/BU-ISCIII/plasmidID/blob/master/img/pipeline_pID.png"</span> <span class="na" style="color: #008080;">alt=</span><span class="s" style="color: #d14;">"workflow_small"</span> <span class="na" style="color: #008080;">width=</span><span class="s" style="color: #d14;">"500"</span><span class="nt" style="color: #000080;">></span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="markdown"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="markdown"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="markdown"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown"></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Docker</span></span>
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24
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="markdown"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="gh" style="color: #999;"># Quick usage</span></span>
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26
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="markdown">Example:</span>
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27
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="markdown">Clone the repo:</span>
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28
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="markdown"><span class="p">```</span><span class="nl">Bash</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="228" style="width: 35px; color: rgba(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">@@ -45,7 +228,6 @@ docker run -v $PWD:$PWD -w $PWD buisciii/plasmidid plasmidID.sh \</td>
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45
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -s KPN</span></span>
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46
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="markdown"><span class="p">```</span></span>
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47
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="markdown"></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"></span>
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49
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="markdown">Or you can use Singularity instead:</span>
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50
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="markdown"><span class="p">```</span><span class="nl">Bash</span></span>
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51
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="markdown"><span class="sb" style="color: #d14;">singularity exec docker://buisciii/plasmidid plasmidID.sh \</span></span>
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<li id="5013f78c1a777b3328f8fd9f2b51313d209f022c">
<a href="https://salsa.debian.org/med-team/plasmidid/-/commit/14fc856f1e788a910ed2e01e7fc61bd0a313c3a2#5013f78c1a777b3328f8fd9f2b51313d209f022c"><strong>bin/download_plasmid_database.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -148,7 +148,7 @@ def main():</td>
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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">erroneous</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">plasmid_failed_path</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;">ferror</span><span class="p">:</span></span>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">acc</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">erroneous</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">ferror</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">acc</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;">reason</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">ferror</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">acc</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;">reason</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span><span class="p">)</span></span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>
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153
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"ALL DONE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">FASTA file is available in: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">plasmid_fasta_path</span><span class="p">)</span></span>
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154
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/plasmidid/-/commit/14fc856f1e788a910ed2e01e7fc61bd0a313c3a2#8a077ed81785711c0820fbc816c88718ecc7259e"><strong>bin/mashclust.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="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Standard library imports</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</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;">subprocess</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Third party imports</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;">argparse</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span> </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Entrez</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;">=============================================================</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;">HEADER</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;">=============================================================</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;">FUNCTION: Reduces redundancy in multifasta files using kmer mash distance,</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;">takes the longest sequence per cluster as representative</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;">INSTITUTION:CNM-ISCIII</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;">AUTHOR: Pedro J. Sola (pedroscampoy@gmail.com)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">d^v^b</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">VERSION=0.1</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;">CREATED: 27 May 2020</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;">REVISION: </span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;">TODO:</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">================================================================</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;">END_OF_HEADER</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;">================================================================</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">END_FORMATTING</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[0m'</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="n" style="color: #333;">WHITE_BG</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[0;30;47m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="n" style="color: #333;">BOLD</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[1m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="n" style="color: #333;">UNDERLINE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[4m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">RED</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[31m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">GREEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[32m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">MAGENTA</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[35m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">BLUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[34m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">CYAN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[36m'</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">YELLOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[93m'</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">DIM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[2m'</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_create_dir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#exists = os.path.isfile(path)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#exists = os.path.isdir(path)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC58" 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="LC59" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mash_dist</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># mash dist -i database.filtered_0.9_term.fasta database.filtered_0.9_term.fasta > database.filtered_0.9_term.mash.distances.tab</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#'reference_ID', 'query_ID', 'distance', 'p_value', 'shared_hashes'</span></span>
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64
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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="n" style="color: #333;">input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">file_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">).</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">file_prefix</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">output_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".mash.distances.tab"</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">output_filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mash"</span><span class="p">,</span> <span class="s" style="color: #d14;">"dist"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">),</span> <span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">input_file</span><span class="p">]</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">param</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmd</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="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;">output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"w+"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outfile</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#calculate mash distance and save it in output file</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="n" style="color: #333;">universal_newlines</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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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">returncode</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="n" style="color: #333;">GREEN</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Program %s successfully executed"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">END_FORMATTING</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">RED</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BOLD</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Command %s FAILED</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">END_FORMATTING</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BOLD</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"WITH PARAMETERS: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">END_FORMATTING</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="p">)</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>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BOLD</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"EXIT-CODE: %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">returncode</span> <span class="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">"ERROR:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">END_FORMATTING</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">RED</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BOLD</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"failed to execute program '%s': %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">prog</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">END_FORMATTING</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output_file</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mash_dist_to_pairwise</span><span class="p">(</span><span class="n" style="color: #333;">distance_file</span><span class="p">,</span> <span class="n" style="color: #333;">distance_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'hash_distance'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">distance_file</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'reference_ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'query_ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'distance'</span><span class="p">,</span> <span class="s" style="color: #d14;">'p_value'</span><span class="p">,</span> <span class="s" style="color: #d14;">'shared_hashes'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[[</span><span class="s" style="color: #d14;">'hash_1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'hash_2'</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'shared_hashes'</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">,</span> <span class="n" style="color: #333;">expand</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="LC98" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">hash_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">hash_1</span><span class="p">.</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">hash_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">hash_2</span><span class="p">.</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'hash_distance'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">hash_1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">hash_2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">dfpair</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[[</span><span class="s" style="color: #d14;">'reference_ID'</span><span class="p">,</span> <span class="s" style="color: #d14;">'query_ID'</span><span class="p">,</span> <span class="n" style="color: #333;">distance_type</span><span class="p">]]</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dfpair</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pairwise_to_cluster</span><span class="p">(</span><span class="n" style="color: #333;">pw</span><span class="p">,</span><span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span><span class="p">):</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">columns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pw</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">sorted_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pw</span><span class="p">[(</span><span class="n" style="color: #333;">pw</span><span class="p">[</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pw</span><span class="p">[</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]])</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">pw</span><span class="p">[</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">threshold</span><span class="p">)].</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]])</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">pw</span><span class="p">.</span><span class="n" style="color: #333;">head</span><span class="p">())</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">sorted_df</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> </span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rename_dict_clusters</span><span class="p">(</span><span class="n" style="color: #333;">cluster_dict</span><span class="p">):</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">reordered_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cluster_dict</span><span class="p">)):</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">reordered_dict</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reordered_dict</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> </span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">regroup_clusters</span><span class="p">(</span><span class="n" style="color: #333;">list_keys</span><span class="p">,</span> <span class="n" style="color: #333;">groups_dict</span><span class="p">,</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">):</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#sum previous clusters</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">list_keys</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">new_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="n" style="color: #333;">groups_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">list_keys</span><span class="p">],</span> <span class="p">[])</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#add new cluster</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">cluster_asign</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">new_cluster</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">))</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Remove duped cluster</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">first_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list_keys</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">groups_dict</span><span class="p">[</span><span class="n" style="color: #333;">first_cluster</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_asign</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">rest_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list_keys</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rest_cluster</span><span class="p">:</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">groups_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">groups_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rename_dict_clusters</span><span class="p">(</span><span class="n" style="color: #333;">groups_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">groups_dict</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> </span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sorted_df</span><span class="p">.</span><span class="n" style="color: #333;">iterrows</span><span class="p">():</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">sample_1</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;">row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">sample_2</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;">row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">both_samples_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">2</span><span class="p">].</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">both_samples_list</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">all_samples_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="p">[])</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> </span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample_1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_samples_dict</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sample_2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_samples_dict</span><span class="p">:</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#extract cluster which have the new samples</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">key_with_sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">key</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sample_2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="p">)}</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">cluster_with_sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">key_with_sample</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">cluster_with_sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_with_sample</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">number_of_shared_clusters</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">key_with_sample</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">number_of_shared_clusters</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">regroup_clusters</span><span class="p">(</span><span class="n" style="color: #333;">cluster_with_sample</span><span class="p">,</span> <span class="n" style="color: #333;">groups</span><span class="p">,</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">)</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">cluster_with_sample_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">cluster_with_sample_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">))</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">both_samples_list</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> </span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pw</span><span class="p">[(</span><span class="n" style="color: #333;">pw</span><span class="p">[</span><span class="n" style="color: #333;">pw</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pw</span><span class="p">[</span><span class="n" style="color: #333;">pw</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]])</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">pw</span><span class="p">[</span><span class="n" style="color: #333;">pw</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">threshold</span><span class="p">)].</span><span class="n" style="color: #333;">iterrows</span><span class="p">():</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">sample_1</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;">row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">sample_2</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;">row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">all_samples_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="p">[])</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample_1</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;">all_samples_dict</span><span class="p">:</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sample_1</span><span class="p">]</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample_2</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;">all_samples_dict</span><span class="p">:</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sample_2</span><span class="p">]</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">cluster_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">))</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">cluster_df_return</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_df</span><span class="p">.</span><span class="n" style="color: #333;">stack</span><span class="p">().</span><span class="n" style="color: #333;">droplevel</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">reset_index</span><span class="p">().</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'index'</span><span class="p">:</span> <span class="s" style="color: #d14;">'group'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="s" style="color: #d14;">'id'</span><span class="p">})</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cluster_df_return</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">big_pairwise_to_cluster</span><span class="p">(</span><span class="n" style="color: #333;">pw</span><span class="p">,</span><span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span><span class="p">):</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> </span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rename_dict_clusters</span><span class="p">(</span><span class="n" style="color: #333;">cluster_dict</span><span class="p">):</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">reordered_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cluster_dict</span><span class="p">)):</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">reordered_dict</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">reordered_dict</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> </span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">regroup_clusters</span><span class="p">(</span><span class="n" style="color: #333;">list_keys</span><span class="p">,</span> <span class="n" style="color: #333;">groups_dict</span><span class="p">,</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">):</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#sum previous clusters</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">list_keys</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">new_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="n" style="color: #333;">groups_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">list_keys</span><span class="p">],</span> <span class="p">[])</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#add new cluster</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">cluster_asign</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">new_cluster</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Remove duped cluster</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">first_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list_keys</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">groups_dict</span><span class="p">[</span><span class="n" style="color: #333;">first_cluster</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_asign</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">rest_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">list_keys</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="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rest_cluster</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">groups_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">groups_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rename_dict_clusters</span><span class="p">(</span><span class="n" style="color: #333;">groups_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">groups_dict</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC202" 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;">pw</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC203" 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</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">line_split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">sample_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_split</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">sample_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_split</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="LC207" class="line" lang="python"> <span class="n" style="color: #333;">hash1</span><span class="p">,</span> <span class="n" style="color: #333;">hash2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_split</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">hash_distance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">hash1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">hash2</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hash_distance</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">threshold</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">both_samples_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sample_1</span><span class="p">,</span><span class="n" style="color: #333;">sample_2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">both_samples_list</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">all_samples_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="p">[])</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample_1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_samples_dict</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sample_2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_samples_dict</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#extract cluster which have the new samples</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">key_with_sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">key</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">sample_2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">value</span><span class="p">)}</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">cluster_with_sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">key_with_sample</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">cluster_with_sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_with_sample</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">number_of_shared_clusters</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">key_with_sample</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">number_of_shared_clusters</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">regroup_clusters</span><span class="p">(</span><span class="n" style="color: #333;">cluster_with_sample</span><span class="p">,</span> <span class="n" style="color: #333;">groups</span><span class="p">,</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">)</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">cluster_with_sample_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">cluster_with_sample_name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">both_samples_list</span><span class="p">))</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" 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="LC232" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">both_samples_list</span></span>
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<pre style="margin: 0;">+<span id="LC233" 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="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample_1</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;">all_samples_dict</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sample_1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample_2</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;">all_samples_dict</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">group_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">group_number</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sample_2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">cluster_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">groups</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">cluster_df_return</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_df</span><span class="p">.</span><span class="n" style="color: #333;">stack</span><span class="p">().</span><span class="n" style="color: #333;">droplevel</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">reset_index</span><span class="p">().</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'index'</span><span class="p">:</span> <span class="s" style="color: #d14;">'group'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="s" style="color: #d14;">'id'</span><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cluster_df_return</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">calculate_seqlen</span><span class="p">(</span><span class="n" style="color: #333;">fasta_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">len_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span><span class="s" style="color: #d14;">'length'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fasta_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">):</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">len_df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="s" style="color: #d14;">'id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">len_df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="s" style="color: #d14;">'length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index</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="LC255" class="line" lang="python"> <span class="n" style="color: #333;">len_df</span><span class="p">[</span><span class="s" style="color: #d14;">'length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len_df</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">.</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="s" style="color: #d14;">'int'</span><span class="p">)</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">len_df</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_representative</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">clustered</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_length</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">final_cluster</span><span class="p">):</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">final_cluster</span><span class="p">[</span><span class="s" style="color: #d14;">'length'</span><span class="p">][</span><span class="n" style="color: #333;">final_cluster</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">idclust</span><span class="p">].</span><span class="n" style="color: #333;">tolist</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idclust</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">clustered</span><span class="p">]</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lengths</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_distance_legacy</span><span class="p">(</span><span class="n" style="color: #333;">reprensetative</span><span class="p">,</span> <span class="n" style="color: #333;">list_clustered</span><span class="p">,</span> <span class="n" style="color: #333;">pwdist</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">distances</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">pwdist</span><span class="p">[</span><span class="n" style="color: #333;">pwdist</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]][(</span><span class="n" style="color: #333;">pwdist</span><span class="p">[</span><span class="n" style="color: #333;">pwdist</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">reprensetative</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">pwdist</span><span class="p">[</span><span class="n" style="color: #333;">pwdist</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">idclust</span><span class="p">)].</span><span class="n" style="color: #333;">tolist</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idclust</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">list_clustered</span><span class="p">]</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">distances</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_distance</span><span class="p">(</span><span class="n" style="color: #333;">reprensetative</span><span class="p">,</span> <span class="n" style="color: #333;">list_clustered</span><span class="p">,</span> <span class="n" style="color: #333;">mash_file</span><span class="p">):</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">distances</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">idclust</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">list_clustered</span><span class="p">:</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="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;">mash_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" 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</span><span class="p">:</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">line_split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">sample_1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_split</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">sample_2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_split</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sample_1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">reprensetative</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sample_2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">idclust</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">hash1</span><span class="p">,</span> <span class="n" style="color: #333;">hash2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line_split</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">hash_distance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">hash1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">hash2</span><span class="p">))</span> </span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">distances</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">hash_distance</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">distances</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">retrieve_fasta_cluster</span><span class="p">(</span><span class="n" style="color: #333;">fasta_file</span><span class="p">,</span> <span class="n" style="color: #333;">final_cluster</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">mash_file</span><span class="p">,</span> <span class="n" style="color: #333;">kmerdist</span><span class="p">,</span> <span class="n" style="color: #333;">quantity_id</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">save_clustered</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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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">fasta_file</span><span class="p">)</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">file_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">).</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">file_prefix</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> </span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">output_representative</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</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;">kmerdist</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.representative.fasta'</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">output_clustered</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</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;">kmerdist</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.clustered.fasta'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">output_summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</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;">kmerdist</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.clusters.tab'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="n" style="color: #333;">representative_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">final_cluster</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'group'</span><span class="p">,</span> <span class="s" style="color: #d14;">'length'</span><span class="p">],</span> <span class="n" style="color: #333;">ascending</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">]).</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'group'</span><span class="p">).</span><span class="n" style="color: #333;">head</span><span class="p">(</span><span class="n" style="color: #333;">quantity_id</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">summary_id_grouped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">final_cluster</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'group'</span><span class="p">)[</span><span class="s" style="color: #d14;">'id'</span><span class="p">].</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">).</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'clustered'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">representative_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">representative_id</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">representative_and_sumary</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">representative_id</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">summary_id_grouped</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'group'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'left'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Use function extract_representative to remove the repr. from column</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">representative_and_sumary</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="n" style="color: #333;">extract_representative</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">representative_and_sumary</span><span class="p">[</span><span class="s" style="color: #d14;">'lengths_clustered'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">representative_and_sumary</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">extract_length</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">final_cluster</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">representative_and_sumary</span><span class="p">[</span><span class="s" style="color: #d14;">'distance_clustered'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">representative_and_sumary</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">extract_distance</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">clustered</span><span class="p">,</span> <span class="n" style="color: #333;">mash_file</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#read the fasta and retrieve representative sequences</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">representative_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">clustered_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fasta_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">):</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">representative_list</span><span class="p">:</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">representative_records</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">clustered_records</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> </span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">representative_records</span><span class="p">,</span> <span class="n" style="color: #333;">output_representative</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">save_clustered</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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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">clustered_records</span><span class="p">,</span> <span class="n" style="color: #333;">output_clustered</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> </span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">representative_and_sumary</span><span class="p">.</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">output_summary</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">index</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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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">previous_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">final_cluster</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">post_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">representative_and_sumary</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">MAGENTA</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"%s sequences clustered into %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">previous_seq</span><span class="p">,</span> <span class="n" style="color: #333;">post_seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">END_FORMATTING</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> </span>
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325
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_arguments</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'common_mash_reference.py'</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Search for all mash files and find the representative reference'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-i'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--input'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"input_file"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"input_directory"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'REQUIRED.Input FASTA file'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--output'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Output directory to extract clusteres FASTA'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-d'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--distance'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</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;">'Threshold distance to cluster sequences[0-1] 0(identical) 1(unrelated) (default 0.5)'</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;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--output_grouped'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</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;">'Output clustered (non representative sequences'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arguments</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_arguments</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">input_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</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="LC346" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">).</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC347" 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="LC348" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">check_create_dir</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#LOGGING</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Create log file with date and time</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">right_now</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;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">date</span><span class="p">.</span><span class="n" style="color: #333;">today</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">right_now_full</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">right_now</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">log_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'mashclust'</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;">right_now_full</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".log"</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">log_full_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">log_filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">formatter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">(</span><span class="s" style="color: #d14;">'%(asctime)s:%(message)s'</span><span class="p">)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">file_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">FileHandler</span><span class="p">(</span><span class="n" style="color: #333;">log_full_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">file_handler</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">file_handler</span><span class="p">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="n" style="color: #333;">formatter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">stream_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">StreamHandler</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">stream_handler</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#stream_handler.setFormatter(formatter)</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">stream_handler</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">file_handler</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#####################START PIPELINE################</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#CALCULATE MASH DISTANCE</span></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Obtaining mash distance'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">mash_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mash_dist</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Obtaining cluster from distance'</span><span class="p">)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#pairwise_distance = mash_dist_to_pairwise(mash_file)</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#cluster_df = pairwise_to_cluster(pairwise_distance, threshold=args.distance)</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">cluster_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">big_pairwise_to_cluster</span><span class="p">(</span><span class="n" style="color: #333;">mash_file</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">)</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Calculating length'</span><span class="p">)</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">len_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculate_seqlen</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">)</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">final_cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cluster_df</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">len_df</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'left'</span><span class="p">)</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Filtering representative fasta'</span><span class="p">)</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">retrieve_fasta_cluster</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">final_cluster</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">mash_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">distance</span><span class="p">,</span> <span class="n" style="color: #333;">quantity_id</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">save_clustered</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output_grouped</span><span class="p">)</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'DONE'</span><span class="p">)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">exception</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<li id="aa410d7cdf4c86039dd72deb31e6663794fe88a5">
<a href="https://salsa.debian.org/med-team/plasmidid/-/commit/14fc856f1e788a910ed2e01e7fc61bd0a313c3a2#aa410d7cdf4c86039dd72deb31e6663794fe88a5"><strong>bin/spades_assembly.sh</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">@@ -26,19 +26,17 @@ usage() {</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;">spades_assembly script that assemble illumina sequences using SPAdes</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="sh" style="color: #d14;">usage : </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;"> <-p R1_paired file> <-P R2_paired file> [-<span class="idiff left right">u <R1_unpaired>] [-U <R2_unpaired>] [-</span>o <directory>]</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="sh" style="color: #d14;">usage : </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;"> <-p R1_paired file> <-P R2_paired file> [-o <directory>]</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="sh" style="color: #d14;"> [-k <int>][-s sample_name] [-g group_name] [-f <file_name>] [-T <int>] [q] [-c] [-v] [-h]</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="sh" style="color: #d14;"> -p R1_paired file (mandatory)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"><span class="sh" style="color: #d14;"> -P R2_paired file (mandatory)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="sh" style="color: #d14;"> -u R1_unpaired file</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="sh" style="color: #d14;"> -U R2_unpaired file</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="sh" style="color: #d14;"> -k kmers, supplied as numbers sepparated by number or one flag per number, default: 21,33,55,77,99,127</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="sh" style="color: #d14;"> -o output directory (optional)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="sh" style="color: #d14;"> -f file name</span></span>
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39
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="sh" style="color: #d14;"> -s sample name (mandatory)</span></span>
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40
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="sh" style="color: #d14;"> -g group name (optional). If unset, samples will be gathered in NO_GROUP group</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"><span class="sh" style="color: #d14;"> -q quick_mode: look for files in a folder SUPPLIED with "paired" <span class="idiff left right">and "unpaired" </span>term</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="sh" style="color: #d14;"> -q quick_mode: look for files in a folder SUPPLIED with "paired" term</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="sh" style="color: #d14;"> -c clean mode: remove unnecesary temporary folders</span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="sh" style="color: #d14;"> -T threads, default 1</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="sh" style="color: #d14;"> -v version</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">@@ -89,8 +87,6 @@ cwd="$(pwd)"</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="shell"><span class="nv" style="color: #008080;">group</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"NO_GROUP"</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="shell"><span class="nv" style="color: #008080;">r1_paired_file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"R1_paired_file"</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="shell"><span class="nv" style="color: #008080;">r2_paired_file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"R2_paired_file"</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="shell"><span class="nv" style="color: #008080;">r1_unpaired_command</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="shell"><span class="nv" style="color: #008080;">r2_unpaired_command</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="shell"><span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="shell"><span class="nv" style="color: #008080;">kmer_values_command</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"21,33,55,77,99,127"</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"><span class="nv" style="color: #008080;">kmer_option</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,14 +104,6 @@ while getopts $options opt; do</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="shell"> P <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_paired_file</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="shell"> u <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="shell"> <span class="nv" style="color: #008080;">r1_unpaired_file</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="shell"> <span class="nv" style="color: #008080;">r1_unpaired_command</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"--s1"</span> <span class="nv" style="color: #008080;">$r1_unpaired_file</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="shell"> U <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_unpaired_file</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_unpaired_command</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"--s1"</span> <span class="nv" style="color: #008080;">$r2_unpaired_file</span><span class="si" style="color: #d14;">)</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="shell"> <span class="p">;;</span></span>
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119
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="shell"> o <span class="p">)</span></span>
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120
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="shell"> <span class="nv" style="color: #008080;">output_dir</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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121
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="shell"> <span class="p">;;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(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="200" style="width: 35px; color: rgba(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">@@ -212,10 +200,6 @@ if [ $quick_mode = true ]; then</td>
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212
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Entering QUICK MODE"</span></span>
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213
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="shell"> <span class="nv" style="color: #008080;">r1_paired_file</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>find <span class="nv" style="color: #008080;">$directory_reads</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*1_paired.fastq.gz"</span> <span class="nt" style="color: #000080;">-type</span> f<span class="si" style="color: #d14;">)</span></span>
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214
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_paired_file</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>find <span class="nv" style="color: #008080;">$directory_reads</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*2_paired.fastq.gz"</span> <span class="nt" style="color: #000080;">-type</span> f<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="shell"> <span class="nv" style="color: #008080;">r1_unpaired_file</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>find <span class="nv" style="color: #008080;">$directory_reads</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*1_unpaired.fastq.gz"</span> <span class="nt" style="color: #000080;">-type</span> f<span class="si" style="color: #d14;">)</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="shell"> <span class="nv" style="color: #008080;">r1_unpaired_command</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"--s1"</span> <span class="nv" style="color: #008080;">$r1_unpaired_file</span><span class="si" style="color: #d14;">)</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_unpaired_file</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>find <span class="nv" style="color: #008080;">$directory_reads</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*2_unpaired.fastq.gz"</span> <span class="nt" style="color: #000080;">-type</span> f<span class="si" style="color: #d14;">)</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_unpaired_command</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"--s2"</span> <span class="nv" style="color: #008080;">$r2_unpaired_file</span><span class="si" style="color: #d14;">)</span></span>
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219
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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220
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="shell"></span>
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221
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -231,8 +215,6 @@ echo "$(date)"</td>
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231
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Assembly:"</span></span>
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"R1 paired file = "</span> <span class="nv" style="color: #008080;">$r1_paired_file</span></span>
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233
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"R2 paired file = "</span> <span class="nv" style="color: #008080;">$r2_paired_file</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"R1 unpaired file = "</span> <span class="nv" style="color: #008080;">$r1_unpaired_file</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"R2 unpaired file = "</span> <span class="nv" style="color: #008080;">$r2_unpaired_file</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="shell">spades.py <span class="se" style="color: #d14;">\</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -241,8 +223,6 @@ spades.py \</td>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="shell"><span class="nt" style="color: #000080;">-k</span> <span class="nv" style="color: #008080;">$kmer_values_command</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="shell"><span class="nt" style="color: #000080;">--pe1-1</span> <span class="nv" style="color: #008080;">$r1_paired_file</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="shell"><span class="nt" style="color: #000080;">--pe1-2</span> <span class="nv" style="color: #008080;">$r2_paired_file</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="shell"><span class="nv" style="color: #008080;">$r1_unpaired_command</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="shell"><span class="nv" style="color: #008080;">$r2_unpaired_command</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="shell"><span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"Spades command failed. See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs for more information."</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Standard library imports</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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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;">subprocess</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">html</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Third party imports</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span> </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Entrez</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">tabulate</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">tabulate</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</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="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;">=============================================================</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;">HEADER</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">=============================================================</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;">FUNCTION: Creates a summary report in tsv and hml from plasmidID execution</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;">INSTITUTION:CNM-ISCIII</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">AUTHOR: Pedro J. Sola (pedroscampoy@gmail.com)</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;">d^v^b</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;">VERSION=0.1</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">CREATED: 04 June 2020</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;">REVISION: </span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">TODO:</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;">================================================================</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;">END_OF_HEADER</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;">================================================================</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="n" style="color: #333;">END_FORMATTING</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[0m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="n" style="color: #333;">WHITE_BG</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[0;30;47m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="n" style="color: #333;">BOLD</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[1m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">UNDERLINE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[4m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">RED</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[31m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">GREEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[32m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">MAGENTA</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[35m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">BLUE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[34m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">CYAN</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[36m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">YELLOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[93m'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="n" style="color: #333;">DIM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\033</span><span class="s" style="color: #d14;">[2m'</span></span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_file_exists</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> Check file exist and is not 0 Kb, if not program exit.</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#file_info = os.stat(file_name) #Retrieve the file info to check if has size > 0</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#or file_info.st_size == 0:</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">):</span> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">RED</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BOLD</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"File: %s not found or empty</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">END_FORMATTING</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_files</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">):</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">percentage_file</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="LC68" class="line" lang="python"> <span class="n" style="color: #333;">complete_file</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="LC69" class="line" lang="python"> <span class="n" style="color: #333;">representative_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</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;">for</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">files</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">walk</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">):</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".coverage_adapted_clustered_percentage"</span><span class="p">):</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">percentage_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".plasmids.complete"</span><span class="p">):</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">complete_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"representative"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".fasta"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">representative_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">percentage_file</span><span class="p">,</span> <span class="n" style="color: #333;">complete_file</span><span class="p">,</span> <span class="n" style="color: #333;">representative_file</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">percentage_to_df</span><span class="p">(</span><span class="n" style="color: #333;">percentage_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">percentage_file</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">percentage_file</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;">names</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="s" style="color: #d14;">'percentage'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'percentage'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'percentage'</span><span class="p">].</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span></span>
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<pre style="margin: 0;">+<span id="LC86" 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="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span><span class="s" style="color: #d14;">'percentage'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">len_description_to_df</span><span class="p">(</span><span class="n" style="color: #333;">representative_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span><span class="s" style="color: #d14;">'length'</span><span class="p">,</span><span class="s" style="color: #d14;">'species'</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">representative_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="s" style="color: #d14;">'id'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="s" style="color: #d14;">'length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq_record</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">description_split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_record</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="s" style="color: #d14;">'species'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">).</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">description_split</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">).</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">description_split</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index</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="LC99" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'length'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'length'</span><span class="p">].</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">complete_report_df</span><span class="p">(</span><span class="n" style="color: #333;">complete_file</span><span class="p">,</span> <span class="n" style="color: #333;">len_description_df</span><span class="p">,</span> <span class="n" style="color: #333;">percentage_df</span><span class="p">):</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_to_list</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">listed_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">contig_name</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">listed_set</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">listed_set</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#CP029217.1 176762 288994 9 id=170244</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">dfc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">complete_file</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;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="s" style="color: #d14;">'start'</span><span class="p">,</span> <span class="s" style="color: #d14;">'end'</span><span class="p">,</span> <span class="s" style="color: #d14;">'contig_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'contig_id'</span><span class="p">])</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">dfc</span><span class="p">[</span><span class="s" style="color: #d14;">'len_covered'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfc</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dfc</span><span class="p">.</span><span class="n" style="color: #333;">start</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">covered_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfc</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">)[</span><span class="s" style="color: #d14;">'len_covered'</span><span class="p">].</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">().</span><span class="n" style="color: #333;">reset_index</span><span class="p">()</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">contigs_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfc</span><span class="p">.</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">)[</span><span class="s" style="color: #d14;">'contig_name'</span><span class="p">].</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">).</span><span class="n" style="color: #333;">reset_index</span><span class="p">()</span><span class="c1" style="color: #998; font-style: italic;">#Merge all dataframes </span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Merge all dataframes</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len_description_df</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">covered_df</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'left'</span><span class="p">)</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'fraction_covered'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">len_covered</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'len_covered'</span><span class="p">]</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">contigs_df</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'left'</span><span class="p">)</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">()</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'contig_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">set_to_list</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">percentage_df</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'left'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'length'</span><span class="p">],</span> <span class="n" style="color: #333;">ascending</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;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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="LC124" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">fillna</span><span class="p">(</span><span class="s" style="color: #d14;">'X'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">df</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">include_images</span><span class="p">(</span><span class="n" style="color: #333;">sample_folder</span><span class="p">,</span> <span class="n" style="color: #333;">summary_df</span><span class="p">):</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_folder</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">image_finder</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">sample_folder</span><span class="p">):</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">files</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">walk</span><span class="p">(</span><span class="n" style="color: #333;">sample_folder</span><span class="p">):</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'images'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">root</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.png'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'file://'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">summary_df</span><span class="p">[</span><span class="s" style="color: #d14;">'images'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">summary_df</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">image_finder</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">sample_folder</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">summary_df</span><span class="p">.</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">sample_folder</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;">sample</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_final_results.tab'</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">index</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="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">summary_df</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="n" style="color: #333;">html_template</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="LC140" class="line" lang="python"><span class="s" style="color: #d14;"> <!doctype html></span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"><span class="s" style="color: #d14;"> .summary{</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"><span class="s" style="color: #d14;"> display: flex;</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"><span class="s" style="color: #d14;"> flex-direction: column-reverse;</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="s" style="color: #d14;"> .numeric-values {</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;"> display: flex;</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> flex-direction: row;</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> justify-content: space-around;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> .numeric-values div {</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> flex-grow: 1;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;"> .neutral {</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"><span class="s" style="color: #d14;"> background-color: lightgray;</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"><span class="s" style="color: #d14;"> .likely {</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"><span class="s" style="color: #d14;"> background-color: limegreen;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;"> .unlikely {</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"><span class="s" style="color: #d14;"> background-color: sandybrown;</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;"> .unprobable {</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"><span class="s" style="color: #d14;"> background-color: brown;</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"><span class="s" style="color: #d14;"> header {</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"><span class="s" style="color: #d14;"> display: flex;</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"><span class="s" style="color: #d14;"> flex-direction: row;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;"> justify-content: flex-start;</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="s" style="color: #d14;"> align-items: flex-end;</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;"> font-size: 2.7em;</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;"> table {</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> position: relative;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> border-collapse: collapse; </span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;"> header img {</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> width: 70px;</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;"> th {</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;"> font-size: 1.3em;</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"><span class="s" style="color: #d14;"> position: sticky;</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"><span class="s" style="color: #d14;"> tr td {</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> font-size: 1.1em;</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> footer {</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"><span class="s" style="color: #d14;"> tr:nth-child(even) {background-color: snow;}</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"><span class="s" style="color: #d14;"> tr:hover {background-color:azure;}</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"><span class="s" style="color: #d14;"> <title>PlasmidID Report</title></span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> PlasmidID REPORT</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"><span class="s" style="color: #d14;"> TABLESUMMARY</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"><span class="s" style="color: #d14;"> More information at <a href="https://github.com/BU-ISCIII/plasmidID" target="_blank"> https://github.com/BU-ISCIII/plasmidID </a></span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;"> Author: pedroscampoy@gmail.com (BU-ISCIII)</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"><span class="s" style="color: #d14;"> </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"""</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">summary_to_html</span><span class="p">(</span><span class="n" style="color: #333;">sample_folder</span><span class="p">,</span> <span class="n" style="color: #333;">final_individual_dataframe</span><span class="p">,</span> <span class="n" style="color: #333;">html_template</span><span class="p">):</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">final_individual_dataframe</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_folder</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">html_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sample_folder</span><span class="p">,</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_final_results.html'</span><span class="p">)</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">hidden_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sample_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_final_individual_results.tab'</span><span class="p">)</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> </span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">complete_to_rating</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">fraction_covered</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">0.8</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">fraction_covered</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">1.2</span><span class="p">:</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'likely'</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">fraction_covered</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1.2</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">fraction_covered</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.8</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">fraction_covered</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.5</span><span class="p">):</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'unlikely'</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'unprobable'</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> </span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mapping_to_rating</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'X'</span><span class="p">:</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'neutral'</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">80</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'likely'</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">80</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">percentage</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">60</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'unlikely'</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'unprobable'</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> </span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">apply_img_tag</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'<div class=summary>'</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="o" style="font-weight: 600;">+</span> \</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="s" style="color: #d14;">'<div class=numeric-values>'</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="o" style="font-weight: 600;">+</span> \</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="s" style="color: #d14;">'<div class=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">percentage '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">perc_rating</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'MAPPING %<br>'</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;">row</span><span class="p">.</span><span class="n" style="color: #333;">percentage</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</div>'</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="o" style="font-weight: 600;">+</span> \</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="s" style="color: #d14;">'<div class=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">complete '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">complete_rating</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'ALIGN FR<br>'</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;">row</span><span class="p">.</span><span class="n" style="color: #333;">fraction_covered</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</div>'</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="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="s" style="color: #d14;">'</div>'</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="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="s" style="color: #d14;">'<a href='</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">images</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' target=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">_blank</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">>'</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="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="s" style="color: #d14;">'<img src='</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">images</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' alt='</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</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="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="s" style="color: #d14;">'</a>'</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="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="s" style="color: #d14;">'</div>'</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">italic_species</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'<i>'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">species</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</i>'</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'perc_rating'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">mapping_to_rating</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'complete_rating'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">complete_to_rating</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'images'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">apply_img_tag</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'species'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">italic_species</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">),</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">([</span><span class="s" style="color: #d14;">'percentage'</span><span class="p">,</span> <span class="s" style="color: #d14;">'fraction_covered'</span><span class="p">,</span> <span class="s" style="color: #d14;">'perc_rating'</span><span class="p">,</span> <span class="s" style="color: #d14;">'complete_rating'</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">inplace</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="LC306" class="line" lang="python"></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'images'</span><span class="p">:</span><span class="n" style="color: #333;">sample</span><span class="p">},</span> <span class="n" style="color: #333;">inplace</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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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> </span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">hidden_filename</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">index</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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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tabulate</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'keys'</span><span class="p">,</span> <span class="n" style="color: #333;">tablefmt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'html'</span><span class="p">,</span> <span class="n" style="color: #333;">showindex</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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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">html</span><span class="p">.</span><span class="n" style="color: #333;">unescape</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"style=</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">text-align: right;</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> </span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">final_html</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">html_template</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'TABLESUMMARY'</span><span class="p">,</span> <span class="n" style="color: #333;">table</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;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">html_filename</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</span><span class="p">:</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">final_html</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">summary_to_html_group</span><span class="p">(</span><span class="n" style="color: #333;">group_folder</span><span class="p">,</span> <span class="n" style="color: #333;">html_template</span><span class="p">):</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_folder</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">html_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">group_folder</span><span class="p">,</span> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_final_results.html'</span><span class="p">)</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">individual_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">files</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">walk</span><span class="p">(</span><span class="n" style="color: #333;">group_folder</span><span class="p">):</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"final_individual_results.tab"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">):</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">individual_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">individual_dfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">sample_list_column</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">individual_files</span><span class="p">:</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">'contig_name'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">individual_dfs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">sample_list_column</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">individual_dfs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">df_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">individual_dfs</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="LC337" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">df_</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span><span class="s" style="color: #d14;">'length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'species'</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">],</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'outer'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">coun_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">([</span><span class="s" style="color: #d14;">'length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'species'</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">).</span><span class="n" style="color: #333;">count</span><span class="p">().</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">coun_df</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'outer'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">columns_reorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span><span class="s" style="color: #d14;">'length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'species'</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">,</span> <span class="s" style="color: #d14;">'N'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sample_list_column</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">[</span><span class="n" style="color: #333;">columns_reorder</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">fillna</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="n" style="color: #333;">inplace</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="LC348" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'N'</span><span class="p">,</span><span class="s" style="color: #d14;">'length'</span><span class="p">],</span> <span class="n" style="color: #333;">ascending</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="bp" style="color: #999;">False</span><span class="p">]).</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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="LC350" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tabulate</span><span class="p">(</span><span class="n" style="color: #333;">dfm</span><span class="p">,</span> <span class="n" style="color: #333;">headers</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'keys'</span><span class="p">,</span> <span class="n" style="color: #333;">tablefmt</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'html'</span><span class="p">,</span> <span class="n" style="color: #333;">showindex</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="LC352" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">html</span><span class="p">.</span><span class="n" style="color: #333;">unescape</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">)</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> </span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">final_html</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">html_template</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'TABLESUMMARY'</span><span class="p">,</span> <span class="n" style="color: #333;">table</span><span class="p">)</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> </span>
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356
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<pre style="margin: 0;">+<span id="LC356" 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;">html_filename</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</span><span class="p">:</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">final_html</span><span class="p">)</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> </span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dfm</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> </span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">summary_to_tab_group</span><span class="p">(</span><span class="n" style="color: #333;">group_folder</span><span class="p">):</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">group_folder</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">tab_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">group_folder</span><span class="p">,</span> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_final_results.tab'</span><span class="p">)</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">individual_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">files</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">walk</span><span class="p">(</span><span class="n" style="color: #333;">group_folder</span><span class="p">):</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"final_results.tab"</span><span class="p">):</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">individual_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">individual_dfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">individual_files</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_final_results.tab'</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">([</span><span class="s" style="color: #d14;">'contig_name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'images'</span><span class="p">],</span> <span class="n" style="color: #333;">axis</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">inplace</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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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'fraction_covered'</span><span class="p">:</span><span class="s" style="color: #d14;">'Fr_cov_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="s" style="color: #d14;">'percentage'</span><span class="p">:</span><span class="s" style="color: #d14;">'Map%_'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sample</span><span class="p">},</span> <span class="n" style="color: #333;">inplace</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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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">individual_dfs</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">individual_dfs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">df_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">individual_dfs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">df_</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span><span class="s" style="color: #d14;">'length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'species'</span><span class="p">,</span> <span class="s" style="color: #d14;">'description'</span><span class="p">],</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'outer'</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">count_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">regex</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Fr_cov.*|^id$'</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">groupby</span><span class="p">(</span><span class="s" style="color: #d14;">'id'</span><span class="p">).</span><span class="n" style="color: #333;">count</span><span class="p">().</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">).</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">merge</span><span class="p">(</span><span class="n" style="color: #333;">count_df</span><span class="p">,</span> <span class="n" style="color: #333;">on</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'id'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'outer'</span><span class="p">)</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> </span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">columns_reorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">columns_reorder</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">columns_reorder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">columns_reorder</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">.</span><span class="n" style="color: #333;">tolist</span><span class="p">()[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">[</span><span class="n" style="color: #333;">columns_reorder</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">sort_values</span><span class="p">(</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'N'</span><span class="p">,</span><span class="s" style="color: #d14;">'length'</span><span class="p">],</span> <span class="n" style="color: #333;">ascending</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="bp" style="color: #999;">False</span><span class="p">]).</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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="LC393" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">dfm</span><span class="p">.</span><span class="n" style="color: #333;">to_csv</span><span class="p">(</span><span class="n" style="color: #333;">tab_filename</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;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">index</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="LC395" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_arguments</span><span class="p">():</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">prog</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'summary_report_pid.py'</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Creates a summary report in tsv and hml from plasmidID execution'</span><span class="p">)</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-i'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--input'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"input_folder"</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;">"input_folder"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'REQUIRED.Input pID folder'</span><span class="p">)</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--group'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</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_false'</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;">'Creates a group report instead of individual (Default True)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">arguments</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arguments</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_arguments</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">input_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">input_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#output_dir = input_folder</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#LOGGING</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Create log file with date and time</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#right_now = str(datetime.date.today())</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#right_now_full = "_".join(right_now.split(" "))</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#log_filename = 'logs/summary_pid' + "_" + right_now_full + ".log"</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#log_full_path = os.path.join(output_dir, log_filename)</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#formatter = logging.Formatter('%(asctime)s:%(message)s')</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#file_handler = logging.FileHandler(log_full_path)</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#file_handler.setLevel(logging.DEBUG)</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#file_handler.setFormatter(formatter)</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">stream_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">StreamHandler</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">stream_handler</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#stream_handler.setFormatter(formatter)</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">stream_handler</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#logger.addHandler(file_handler)</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#####################START PIPELINE################</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#CALCULATE MASH DISTANCE</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Creating summary'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">group</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="LC449" class="line" lang="python"> <span class="n" style="color: #333;">summary_to_html_group</span><span class="p">(</span><span class="n" style="color: #333;">input_folder</span><span class="p">,</span> <span class="n" style="color: #333;">html_template</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">summary_to_tab_group</span><span class="p">(</span><span class="n" style="color: #333;">input_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">percentage_file</span><span class="p">,</span> <span class="n" style="color: #333;">complete_file</span><span class="p">,</span> <span class="n" style="color: #333;">representative_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extract_files</span><span class="p">(</span><span class="n" style="color: #333;">input_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">check_file_exists</span><span class="p">(</span><span class="n" style="color: #333;">complete_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">check_file_exists</span><span class="p">(</span><span class="n" style="color: #333;">representative_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">percentage_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">percentage_to_df</span><span class="p">(</span><span class="n" style="color: #333;">percentage_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">len_description_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len_description_to_df</span><span class="p">(</span><span class="n" style="color: #333;">representative_file</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;">summary_df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">complete_report_df</span><span class="p">(</span><span class="n" style="color: #333;">complete_file</span><span class="p">,</span> <span class="n" style="color: #333;">len_description_df</span><span class="p">,</span> <span class="n" style="color: #333;">percentage_df</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">final_individual_dataframe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">include_images</span><span class="p">(</span><span class="n" style="color: #333;">input_folder</span><span class="p">,</span> <span class="n" style="color: #333;">summary_df</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">summary_to_html</span><span class="p">(</span><span class="n" style="color: #333;">input_folder</span><span class="p">,</span> <span class="n" style="color: #333;">final_individual_dataframe</span><span class="p">,</span> <span class="n" style="color: #333;">html_template</span><span class="p">)</span></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="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'DONE'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC464" 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="LC465" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">exception</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ set -e</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#INSTITUTION:ISCIII</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#CENTRE:BU-ISCIII</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#AUTHOR: Pedro J. Sola (pedroscampoy@gmail.com)</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span>1.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span>1.<span class="idiff left right">6.3</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#CREATED: 15 March 2018</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#ACKNOLEDGE: longops2getops.sh: https://gist.github.com/adamhotep/895cebf290e95e613c006afbffef09d7</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">@@ -52,7 +52,7 @@ usage : $0 <-1 R1> <-2 R2> <-d database(fasta)> <-s sample_name> [-g group_name]</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"><span class="sh" style="color: #d14;"> --explore Relaxes default parameters to find less reliable relationships within data supplied and database</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="sh" style="color: #d14;"> --only-reconstruct Database supplied will not be filtered and all sequences will be used as scaffold</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"><span class="sh" style="color: #d14;"> This option does not require R1 and R2, instead a contig file can be supplied</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="sh" style="color: #d14;"> -w Undo winner takes it all algorithm when clustering by kmer - QUICKER MODE</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"><span class="sh" style="color: #d14;"> Trimming:</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"><span class="sh" style="color: #d14;"> --trimmomatic-directory Indicate directory holding trimmomatic .jar executable</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="sh" style="color: #d14;"> --no-trim Reads supplied will not be quality trimmed</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">@@ -60,12 +60,12 @@ usage : $0 <-1 R1> <-2 R2> <-d database(fasta)> <-s sample_name> [-g group_name]</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"><span class="sh" style="color: #d14;"> Coverage and Clustering:</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"><span class="sh" style="color: #d14;"> -C | --coverage-cutoff <int> minimun coverage percentage to select a plasmid as scafold (0-100), default 80</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="sh" style="color: #d14;"> -S | --coverage-summary <int> minimun coverage percentage to include plasmids in summary image (0-100), default 90</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="shell"><span class="sh" style="color: #d14;"> -f | --cluster <int> <span class="idiff left right">identity percentage to cluster plasmids into the same representative sequence (0-100), default 80</span></span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="shell"><span class="sh" style="color: #d14;"> -k | --kmer <int> identity to filter plasmids from the database with kmer approach (0-1), default 0.9</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="sh" style="color: #d14;"> -f | --cluster <int> <span class="idiff left right">kmer identity to cluster plasmids into the same representative sequence (0 means identical) (0-1), default 0.5</span></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="sh" style="color: #d14;"> -k | --kmer <int> identity to filter plasmids from the database with kmer approach (0-1), default 0.9<span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="sh" style="color: #d14;"> Contig local alignment</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"><span class="sh" style="color: #d14;"> -i | --alignment-identity <int> minimun identity percentage aligned for a contig to annotate, default 90</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="shell"><span class="sh" style="color: #d14;"> -l | --alignment-percentage <int> minimun length percentage aligned for a contig to annotate, default <span class="idiff left right">3</span>0</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="sh" style="color: #d14;"> -l | --alignment-percentage <int> minimun length percentage aligned for a contig to annotate, default <span class="idiff left right">2</span>0</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"><span class="sh" style="color: #d14;"> -L | --length-total <int> minimun alignment length to filter blast analysis</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"><span class="sh" style="color: #d14;"> --extend-annotation <int> look for annotation over regions with no homology found (base pairs), default 500bp</span></span>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"></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">@@ -174,22 +174,21 @@ max_memory=4000</td>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="shell"><span class="nv" style="color: #008080;">cwd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="shell"><span class="nv" style="color: #008080;">group</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"NO_GROUP"</span></span>
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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
176
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="shell"><span class="nv" style="color: #008080;">database</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Database"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="shell"><span class="nv" style="color: #008080;">kmer_cutoff</span><span class="o" style="font-weight: 600;">=</span>0.9</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="shell"><span class="nv" style="color: #008080;">kmer_cutoff</span><span class="o" style="font-weight: 600;">=</span>0.9<span class="idiff left right">5</span></span>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="shell"><span class="nv" style="color: #008080;">coverage_cutoff</span><span class="o" style="font-weight: 600;">=</span>80</span>
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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="shell"><span class="nv" style="color: #008080;">coverage_summary</span><span class="o" style="font-weight: 600;">=</span>80</span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="shell"><span class="nv" style="color: #008080;">cluster_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">80</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="shell"><span class="nv" style="color: #008080;">cluster_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">0.5</span></span>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="shell"><span class="nv" style="color: #008080;">alignment_identity</span><span class="o" style="font-weight: 600;">=</span>90</span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="shell"><span class="nv" style="color: #008080;">alignment_percentage</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">3</span>0</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="shell"><span class="nv" style="color: #008080;">alignment_percentage</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">2</span>0</span>
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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="shell"><span class="nv" style="color: #008080;">extend_annotation</span><span class="o" style="font-weight: 600;">=</span>500</span>
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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="shell"><span class="nv" style="color: #008080;">R1</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"R1_file"</span></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="shell"><span class="nv" style="color: #008080;">R2</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"R2_file"</span></span>
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186
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="shell"><span class="nv" style="color: #008080;">no_trim</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="shell"><span class="nv" style="color: #008080;">only_reconstruct</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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<td class="diff-line-num old_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">
188
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="shell"><span class="nv" style="color: #008080;">explore</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
189
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="shell"><span class="nv" style="color: #008080;">include_assembly</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span></span>
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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
190
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="shell"><span class="nv" style="color: #008080;">annotation</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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191
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="shell"><span class="nv" style="color: #008080;">verbose_option_circos</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="shell"><span class="nv" style="color: #008080;">w_winner</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="shell"><span class="nv" style="color: #008080;">w_winner</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"<span class="idiff left right">-w</span>"</span></span>
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193
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="shell"><span class="nv" style="color: #008080;">is_verbose</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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194
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="shell"><span class="nv" style="color: #008080;">config_dir</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$script_dir</span><span class="s2" style="color: #d14;">/config_files"</span></span>
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195
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="shell"><span class="nv" style="color: #008080;">trimmomatic_directory</span><span class="o" style="font-weight: 600;">=</span>/opt/Trimmomatic/</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">@@ -256,7 +255,6 @@ while getopts $options opt; do</td>
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256
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="shell"> R <span class="p">)</span></span>
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257
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="shell"> <span class="nv" style="color: #008080;">only_reconstruct</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span></span>
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258
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">no_trim</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="nv" style="color: #008080;">reconstruct_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$database</span></span>
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260
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="shell"> <span class="p">;;</span></span>
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261
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="shell"> C <span class="p">)</span></span>
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262
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="shell"> <span class="nv" style="color: #008080;">coverage_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -289,7 +287,7 @@ while getopts $options opt; do</td>
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289
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="shell"> <span class="nv" style="color: #008080;">output_dir</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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290
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="shell"> <span class="p">;;</span></span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="shell"> w<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="shell"> <span class="nv" style="color: #008080;">w_winner</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"<span class="idiff left right">-w</span>"</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="shell"> <span class="nv" style="color: #008080;">w_winner</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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293
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="shell"> <span class="p">;;</span></span>
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294
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="shell"> V<span class="p">)</span></span>
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295
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="shell"> <span class="nv" style="color: #008080;">verbose_option_circos</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-V"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="333" style="width: 35px; color: rgba(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="331" style="width: 35px; color: rgba(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">@@ -333,19 +331,26 @@ printf "${YELLOW}Starting plasmidID version:${VERSION}${NC}\n"</td>
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333
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="shell"><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"%s"</span></span>
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334
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="shell"><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">YELLOW</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">------------------</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$r1_file</span> <span class="nt" style="color: #000080;">-a</span> <span class="nt" style="color: #000080;">-z</span> <span class="nv" style="color: #008080;">$r1_file</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$contigs</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">only_reconstruct</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">only_reconstruct</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$only_reconstruct</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##CHECK DEPENDENCIES, MANDATORY FIELDS, FOLDERS AND ARGUMENTS</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">CHECKING DEPENDENCIES AND MANDATORY FILES</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="shell"> check_dependencies.sh blastn bowtie2-build bowtie2 <span class="idiff left right">cd-hit-est </span>bedtools prokka samtools mash circos</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="shell"> check_dependencies.sh blastn bowtie2-build bowtie2 bedtools prokka samtools mash circos</span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="shell"> check_mandatory_files.sh <span class="nv" style="color: #008080;">$r1_file</span> <span class="nv" style="color: #008080;">$r2_file</span> <span class="nv" style="color: #008080;">$database</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="shell"></span>
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349
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: #008080;">$sample</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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350
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">RED</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">ERROR</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">: please, provide a sample name"</span></span>
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351
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="shell"> usage</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -384,8 +389,9 @@ fi</td>
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384
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="shell"></span>
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385
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$explore</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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386
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">coverage_cutoff</span><span class="o" style="font-weight: 600;">=</span>60</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="shell"> <span class="nv" style="color: #008080;">kmer_cutoff</span><span class="o" style="font-weight: 600;">=</span>0.9</span>
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387
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="shell"> <span class="nv" style="color: #008080;">coverage_summary</span><span class="o" style="font-weight: 600;">=</span>70</span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="shell"> <span class="nv" style="color: #008080;">cluster_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">70</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="shell"> <span class="nv" style="color: #008080;">cluster_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">0.3</span></span>
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389
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="shell"> <span class="nv" style="color: #008080;">alignment_percentage</span><span class="o" style="font-weight: 600;">=</span>10</span>
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390
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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391
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="459" style="width: 35px; color: rgba(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="465" style="width: 35px; color: rgba(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">@@ -459,39 +465,38 @@ fi</td>
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459
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465
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="shell"></span>
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460
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466
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">####TRIMMING#################################################################</span></span>
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461
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#############################################################################</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$only_reconstruct</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$no_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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462
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="shell"></span>
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463
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$no_trim</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">then</span></span></span>
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464
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">r1_file_mapping</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$r1_file</span></span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_file_mapping</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$r2_file</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">r1_file_mapping</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$r1_file</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_file_mapping</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$r2_file</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">TRIMMING READS</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="shell"><span class="s2" style="color: #d14;"> Reads will be quality trimmed with a window of 4 and an average quality of 20"</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "R1:" $r1_file</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "R2:" $r2_file</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">TRIMMING READS</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="shell"><span class="s2" style="color: #d14;">Reads will be quality trimmed with a window of 4 and an average quality of 20"</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "R1:" $r1_file</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#echo "R2:" $r2_file</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="shell"> check_dependencies.sh trimmomatic</span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="shell"> <span class="idiff left right">check_dependencies.sh trimmomatic</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="shell"> <span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff">filestrimmed</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="si" style="color: #d14;"><span class="idiff">$(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">ls</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$output_dir</span></span><span class="idiff">/</span><span class="nv" style="color: #008080;"><span class="idiff">$group</span></span><span class="idiff">/</span><span class="nv" style="color: #008080;"><span class="idiff">$sample</span></span><span class="idiff">/trimmed 2> /dev/null | </span><span class="nb" style="color: #0086b3;"><span class="idiff">grep</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"paired"</span></span><span class="idiff"> | </span><span class="nb" style="color: #0086b3;"><span class="idiff">wc</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-l</span></span><span class="si" style="color: #d14;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="shell"> <span class="nv" style="color: #008080;">filestrimmed</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/trimmed 2> /dev/null | <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"paired"</span> | <span class="nb" style="color: #0086b3;">wc</span> <span class="nt" style="color: #000080;">-l</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="shell"></span>
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478
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$filestrimmed</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"4"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span></span>
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479
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Found trimmed files for this sample"</span> <span class="nv" style="color: #008080;">$sample</span><span class="p">;</span></span>
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480
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Omitting trimming"</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$filestrimmed</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"4"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Found trimmed files for this sample"</span> <span class="nv" style="color: #008080;">$sample</span><span class="p">;</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Omitting trimming"</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>quality_trim.sh <span class="nt" style="color: #000080;">-1</span> <span class="nv" style="color: #008080;">$r1_file</span> <span class="nt" style="color: #000080;">-2</span> <span class="nv" style="color: #008080;">$r2_file</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$sample</span> <span class="nt" style="color: #000080;">-g</span> <span class="nv" style="color: #008080;">$group</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/trimmed <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$trimmomatic_directory</span> <span class="nt" style="color: #000080;">-T</span> <span class="nv" style="color: #008080;">$threads</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information. </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command: </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> quality_trim.sh -1 </span><span class="nv" style="color: #008080;">$r1_file</span><span class="s2" style="color: #d14;"> -2 </span><span class="nv" style="color: #008080;">$r2_file</span><span class="s2" style="color: #d14;"> -s </span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -g </span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;"> -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/trimmed -d </span><span class="nv" style="color: #008080;">$trimmomatic_directory</span><span class="s2" style="color: #d14;"> -T </span><span class="nv" style="color: #008080;">$threads</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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481
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="shell"><span class="k" style="font-weight: 600;"> else</span></span>
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482
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<td class="diff-line-num new_line old" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>quality_trim.sh <span class="nt" style="color: #000080;">-1</span> <span class="nv" style="color: #008080;">$r1_file</span> <span class="nt" style="color: #000080;">-2</span> <span class="nv" style="color: #008080;">$r2_file</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$sample</span> <span class="nt" style="color: #000080;">-g</span> <span class="nv" style="color: #008080;">$group</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/trimmed <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$trimmomatic_directory</span> <span class="nt" style="color: #000080;">-T</span> <span class="nv" style="color: #008080;">$threads</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information. </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command: </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> quality_trim.sh -1 </span><span class="nv" style="color: #008080;">$r1_file</span><span class="s2" style="color: #d14;"> -2 </span><span class="nv" style="color: #008080;">$r2_file</span><span class="s2" style="color: #d14;"> -s </span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -g </span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;"> -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/trimmed -d </span><span class="nv" style="color: #008080;">$trimmomatic_directory</span><span class="s2" style="color: #d14;"> -T </span><span class="nv" style="color: #008080;">$threads</span><span class="s2" style="color: #d14;">"</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">No trim selected, skipping trimming step"</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="shell"> <span class="nv" style="color: #008080;">r1_file_mapping</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$r1_file</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_file_mapping</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$r2_file</span></span>
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483
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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485
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">No trim selected, skipping trimming step"</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="shell"> <span class="nv" style="color: #008080;">r1_file_mapping</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$r1_file</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="shell"> <span class="nv" style="color: #008080;">r2_file_mapping</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$r2_file</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_1_paired.fastq.gz</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_1_unpaired.fastq.gz</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_2_paired.fastq.gz</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_2_unpaired.fastq.gz</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_1_paired.fastq.gz</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_1_unpaired.fastq.gz</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_2_paired.fastq.gz</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#group/sample/trimmed/sample_2_unpaired.fastq.gz</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">####ASSEMLY##################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#############################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="shell"></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">@@ -529,7 +534,7 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="shell"></span>
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530
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$only_reconstruct</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="shell"></span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">reconstruct_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_filtered_"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"_term.fasta"</span><span class="idiff left">_</span><span class="nv" style="color: #008080;"><span class="idiff right">$cluster_cutoff</span></span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">reconstruct_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_filtered_"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"_term.fasta"</span></span>
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533
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="shell"></span>
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534
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="shell"></span>
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535
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">####### PREVIOUS SUMMARY OUTPUT########################</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -577,17 +582,26 @@ printf '%s\n' "${variables[$i]}"</td>
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577
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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578
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="shell"></span>
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579
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="shell"></span>
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580
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<td class="diff-line-num new_line old" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">YELLOW</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> STARTING KMER FILTERING, <span class="idiff left right">MAPPING and CLUSTERING</span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">YELLOW</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> STARTING KMER FILTERING, <span class="idiff left right">CLUSTERING and MAPPING </span></span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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581
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="shell"></span>
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582
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="shell"></span>
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583
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">SCREENING READS WITH KMERS</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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584
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<td class="diff-line-num new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="shell"><span class="s2" style="color: #d14;">Reads will be screened against database supplied for further filtering and mapping,</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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585
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="shell"><span class="s2" style="color: #d14;">this will reduce the input sequences to map against"</span> <span class="nv" style="color: #008080;">$sample</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.msh <span class="nt" style="color: #000080;">-a</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.screen.tab <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Found a kmer file for sample"</span> <span class="nv" style="color: #008080;">$sample</span><span class="p">;</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Omitting mash execution"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>mash_screener.sh <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$database</span> <span class="nt" style="color: #000080;">-1</span> <span class="nv" style="color: #008080;">$r1_file_mapping</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$sample</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$kmer_cutoff</span> <span class="nv" style="color: #008080;">$w_winner</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> command: </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">mash_screener.sh -d </span><span class="nv" style="color: #008080;">$database</span><span class="s2" style="color: #d14;"> -1 </span><span class="nv" style="color: #008080;">$r1_file_mapping</span><span class="s2" style="color: #d14;"> -s </span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/kmer"</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#output_dir/$group/$sample/kmer/database.filtered_$kmer_cutoff"_term.fasta"</span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="shell"> mash_screener.sh <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$database</span> <span class="nt" style="color: #000080;">-1</span> <span class="nv" style="color: #008080;">$r1_file_mapping</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$sample</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$kmer_cutoff</span> <span class="nv" style="color: #008080;">$w_winner</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> command: </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">mash_screener.sh -d </span><span class="nv" style="color: #008080;">$database</span><span class="s2" style="color: #d14;"> -1 </span><span class="nv" style="color: #008080;">$r1_file_mapping</span><span class="s2" style="color: #d14;"> -s </span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/kmer"</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="shell"></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">CLUSTERING SEQUENCES BY KMER DISTANCE</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="shell"><span class="s2" style="color: #d14;">Sequences obtained after screen will be clustered to reduce redundancy,</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="shell"><span class="s2" style="color: #d14;">one representative, the largest, will be considered for further analysis"</span> <span class="nv" style="color: #008080;">$sample</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="shell"> mashclust.py <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.filtered_<span class="nv" style="color: #008080;">$kmer_cutoff</span><span class="s2" style="color: #d14;">"_term.fasta"</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$cluster_cutoff</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> command:mashclust.py -i </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/kmer/database.filtered_</span><span class="nv" style="color: #008080;">$kmer_cutoff</span><span class="s2" style="color: #d14;">"</span>_term.fasta<span class="s2" style="color: #d14;">" -d </span><span class="nv" style="color: #008080;">$cluster_cutoff</span><span class="s2" style="color: #d14;">"</span></span>
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589
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="shell"></span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="shell"> <span class="nv" style="color: #008080;">screened_ddbb</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.filtered_<span class="nv" style="color: #008080;">$kmer_cutoff</span><span class="s2" style="color: #d14;">"_term.fasta"</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="shell"> <span class="nv" style="color: #008080;">screened_ddbb</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.filtered_<span class="nv" style="color: #008080;">$kmer_cutoff</span><span class="s2" style="color: #d14;">"_term.<span class="idiff left">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$cluster_cutoff</span></span><span class="s2" style="color: #d14;"><span class="idiff right">".representative.</span>fasta"</span></span>
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591
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="shell"> </span>
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592
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">####MAPPING##################################################################</span></span>
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#############################################################################</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">@@ -646,7 +660,7 @@ will pass to further analysis"</td>
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#sample.coverage_adapted</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#sample.coverage_adapted_filtered_80</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="shell"> filter_fasta.sh <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$database</span> <span class="nt" style="color: #000080;">-f</span> <span class="idiff left right"> </span><span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_filtered_"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">filter_fasta.sh -i </span><span class="nv" style="color: #008080;">$database</span><span class="s2" style="color: #d14;"> -f </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/mapping/</span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.coverage_adapted_filtered_</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="shell"> filter_fasta.sh <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$database</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_filtered_"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">filter_fasta.sh -i </span><span class="nv" style="color: #008080;">$database</span><span class="s2" style="color: #d14;"> -f </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/mapping/</span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.coverage_adapted_filtered_</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#sample.coverage_adapted_filtered_50_term.fasta</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="shell"></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">@@ -658,20 +672,7 @@ will pass to further analysis"</td>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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673
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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674
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">CLUSTERING PUTATIVE PLASMIDS</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="shell"><span class="s2" style="color: #d14;">Clustering by homology removes database redundancy, taking the longest representative of each group.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="shell"><span class="s2" style="color: #d14;">Clusters will be composed by plasmids with an identity of"</span> <span class="nv" style="color: #008080;">$cluster_cutoff</span><span class="s2" style="color: #d14;">"% or higher"</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="shell"></span>
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665
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_filtered_"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"_term.fasta_"</span><span class="nv" style="color: #008080;">$cluster_cutoff</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Found a clustered file for sample"</span> <span class="nv" style="color: #008080;">$sample</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Omitting clustering"</span></span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>cdhit_cluster.sh <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_filtered_"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"_term.fasta"</span> <span class="nt" style="color: #000080;">-c</span> <span class="nv" style="color: #008080;">$cluster_cutoff</span> <span class="nt" style="color: #000080;">-M</span> <span class="nv" style="color: #008080;">$max_memory</span> <span class="nt" style="color: #000080;">-T</span> <span class="nv" style="color: #008080;">$threads</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">cdhit_cluster.sh -i </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/mapping/</span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.coverage_adapted_filtered_</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">_term.fasta</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> -c </span><span class="nv" style="color: #008080;">$cluster_cutoff</span><span class="s2" style="color: #d14;"> -M </span><span class="nv" style="color: #008080;">$max_memory</span><span class="s2" style="color: #d14;"> -T </span><span class="nv" style="color: #008080;">$threads</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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672
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="shell"></span>
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674
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>process_cluster_output.sh <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$reconstruct_fasta</span> <span class="nt" style="color: #000080;">-b</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted"</span> <span class="nt" style="color: #000080;">-c</span> <span class="nv" style="color: #008080;">$coverage_cutoff</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">process_cluster_output.sh -i </span><span class="nv" style="color: #008080;">$reconstruct_fasta</span><span class="s2" style="color: #d14;"> -b </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/mapping/</span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.coverage_adapted</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> -c </span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>process_cluster_output.sh <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$reconstruct_fasta</span> <span class="nt" style="color: #000080;">-b</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted"</span> <span class="nt" style="color: #000080;">-c</span> 80 &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">process_cluster_output.sh -i </span><span class="nv" style="color: #008080;">$reconstruct_fasta</span><span class="s2" style="color: #d14;"> -b </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/mapping/</span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.coverage_adapted</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> -c </span><span class="nv" style="color: #008080;">$coverage_cutoff</span><span class="s2" style="color: #d14;">"</span></span>
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675
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676
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="shell"></span>
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676
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data</span>
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677
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/mapping/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_clustered_ac"</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_clustered_ac"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -719,25 +720,42 @@ A bedgraph file containing mapping information for filtered plasmids will be gen</td>
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719
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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720
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#####################################################################################################################################################</span></span>
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721
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##########################ONLY RECONSTRUCT###########################################################################################################</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#####################################################################################################################################################</span></span>
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#####################################################################################################################################################</span></span>
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723
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="shell"></span>
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="shell"></span>
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725
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BLUE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">ONLY RECONSTRUCT MODE SELECTED</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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726
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="shell"><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">YELLOW</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">WARNING</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">:PlasmidID will not filter the database supplied by coverage,</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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727
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="shell"><span class="s2" style="color: #d14;">instead all sequences supplied by user will be used as scaffold.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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728
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="shell"><span class="s2" style="color: #d14;">Please use a fasta file with limited ammount of sequences."</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BLUE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">SMRT/CONTIG MODE SELECTED</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="shell"><span class="s2" style="color: #d14;">PlasmidID will only use contigs supplied and will not filter by mapping coverage</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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729
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="shell"></span>
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730
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##CHECK DEPENDENCIES, MANDATORY FIELDS, FOLDERS AND ARGUMENTS</span></span>
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="shell"></span>
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732
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">CHECKING DEPENDENCIES AND MANDATORY FILES</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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733
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="shell"></span>
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734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="shell"> check_dependencies.sh blastn prokka circos</span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="shell"> check_dependencies.sh blastn prokka circos<span class="idiff left right"> mash</span></span>
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735
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="shell"></span>
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="shell"> check_mandatory_files.sh <span class="nv" style="color: #008080;">$contigs</span> <span class="nv" style="color: #008080;">$database</span></span>
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737
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737
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="shell"></span>
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738
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="shell"> <span class="nv" style="color: #008080;">config_file_individual</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"OR.conf"</span></span>
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739
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="shell"></span>
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740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="shell"> calculate_seqlen.sh <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$database</span> <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"database_reconstruct_"</span><span class="nv" style="color: #008080;">$sample</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">calculate_seqlen.sh -i </span><span class="nv" style="color: #008080;">$database</span><span class="s2" style="color: #d14;"> -r -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/data -n "</span>database_reconstruct_<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">"</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">SCREENING READS WITH KMERS</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="shell"><span class="s2" style="color: #d14;">Reads will be screened against database supplied for further filtering and mapping,</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="shell"><span class="s2" style="color: #d14;">this will reduce the input sequences to map against"</span> <span class="nv" style="color: #008080;">$sample</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.msh <span class="nt" style="color: #000080;">-a</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.screen.tab <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Found a kmer file for sample"</span> <span class="nv" style="color: #008080;">$sample</span><span class="p">;</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Omitting mash execution"</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>mash_screener.sh <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$database</span> <span class="nt" style="color: #000080;">-1</span> <span class="nv" style="color: #008080;">$contigs</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$sample</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$kmer_cutoff</span> <span class="nv" style="color: #008080;">$w_winner</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> command: </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">mash_screener.sh -d </span><span class="nv" style="color: #008080;">$database</span><span class="s2" style="color: #d14;"> -1 </span><span class="nv" style="color: #008080;">$r1_file_mapping</span><span class="s2" style="color: #d14;"> -s </span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/kmer"</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#output_dir/$group/$sample/kmer/database.filtered_$kmer_cutoff"_term.fasta"</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="shell"></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">CLUSTERING SEQUENCES BY KMER DISTANCE</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="shell"><span class="s2" style="color: #d14;">Sequences obtained after screen will be clustered to reduce redundancy,</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="shell"><span class="s2" style="color: #d14;">one representative, the largest, will be considered for further analysis"</span> <span class="nv" style="color: #008080;">$sample</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="shell"> mashclust.py <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.filtered_<span class="nv" style="color: #008080;">$kmer_cutoff</span><span class="s2" style="color: #d14;">"_term.fasta"</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$cluster_cutoff</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> command: mashclust.py -i </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/kmer/database.filtered_</span><span class="nv" style="color: #008080;">$kmer_cutoff</span><span class="s2" style="color: #d14;">"</span>_term.fasta<span class="s2" style="color: #d14;">" -d </span><span class="nv" style="color: #008080;">$cluster_cutoff</span><span class="s2" style="color: #d14;">"</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="shell"> <span class="nv" style="color: #008080;">screened_ddbb</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/kmer/database.filtered_<span class="nv" style="color: #008080;">$kmer_cutoff</span><span class="s2" style="color: #d14;">"_term."</span><span class="nv" style="color: #008080;">$cluster_cutoff</span><span class="s2" style="color: #d14;">".representative.fasta"</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="shell"></span>
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<td class="diff-line-num new old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="shell"> calculate_seqlen.sh <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$screened_ddbb</span> <span class="nt" style="color: #000080;">-r</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"database_reconstruct_"</span><span class="nv" style="color: #008080;">$sample</span> &>> <span class="nv" style="color: #008080;">$log_file</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">calculate_seqlen.sh -i </span><span class="nv" style="color: #008080;">$database</span><span class="s2" style="color: #d14;"> -r -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/data -n "</span>database_reconstruct_<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">"</span></span>
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741
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<td class="diff-line-num new_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#"database_reconstruct_"$sample.length</span></span>
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<td class="diff-line-num old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
742
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<td class="diff-line-num new_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
743
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<td class="diff-line-num new_line" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{print $1}'</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data/<span class="s2" style="color: #d14;">"database_reconstruct_"</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".length"</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".coverage_adapted_clustered_ac"</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"AWK command fail when creating </span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.coverage_adapted_clustered_ac</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> file .See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">awk '{print </span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">}' </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/data/</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">database_reconstruct_</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.length</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> > </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/data/</span><span class="nv" style="color: #008080;">$sample</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">.coverage_adapted_clustered_ac</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -746,7 +764,7 @@ Please use a fasta file with limited ammount of sequences."</td>
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746
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#sample.karyotype_individual.txt</span></span>
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747
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<td class="diff-line-num new_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#sample.karyotype_individual.txt</span></span>
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748
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="749" 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">
749
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<td class="diff-line-num new_line old" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="shell"> <span class="nv" style="color: #008080;">reconstruct_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$<span class="idiff left right">database</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="shell"> <span class="nv" style="color: #008080;">reconstruct_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$<span class="idiff left">output_dir</span></span><span class="idiff">/</span><span class="nv" style="color: #008080;"><span class="idiff">$group</span></span><span class="idiff">/</span><span class="nv" style="color: #008080;"><span class="idiff">$sample</span></span><span class="idiff">/kmer/database.filtered_</span><span class="nv" style="color: #008080;"><span class="idiff">$kmer_cutoff</span></span><span class="s2" style="color: #d14;"><span class="idiff">"_term."</span></span><span class="nv" style="color: #008080;"><span class="idiff">$cluster_cutoff</span></span><span class="s2" style="color: #d14;"><span class="idiff right">".representative.fasta"</span></span></span>
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750
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<td class="diff-line-num new_line" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
751
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<td class="diff-line-num new_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".bedgraph_term"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
752
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<td class="diff-line-num new_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/data/<span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">".bedgraph_term"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1051" style="width: 35px; color: rgba(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="1069" style="width: 35px; color: rgba(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">@@ -1051,5 +1069,9 @@ draw_circos_images.sh -i $output_dir/$group/$sample \</td>
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1051
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<td class="diff-line-num new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="shell"><span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span>/logs/draw_circos_images.log <span class="se" style="color: #d14;">\</span></span>
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1052
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1070
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="shell"><span class="nt" style="color: #000080;">-c</span> <span class="nv" style="color: #008080;">$verbose_option_circos</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">draw_circos_images.sh -i </span><span class="nv" style="color: #008080;">$output</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -d </span><span class="nv" style="color: #008080;">$config_dir</span><span class="s2" style="color: #d14;"> -C </span><span class="nv" style="color: #008080;">$config_file_individual</span><span class="s2" style="color: #d14;"> -o </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/images -g </span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;"> -s </span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -l </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">/logs/draw_circos_images.log -c </span><span class="nv" style="color: #008080;">$verbose_option_circos</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1053
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<td class="diff-line-num new_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="shell"></span>
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<td class="diff-line-num new old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); 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="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CYAN</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">CREATING SUMMARY REPORT</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> (</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); 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="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="shell"><span class="s2" style="color: #d14;">An html report with miniatures of the images will be generate with useful statistics to determine the correct plasmids in the sample."</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); 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="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="shell"></span>
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<td class="diff-line-num new old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); 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="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="shell">summary_report_pid.py <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$output_dir</span>/<span class="nv" style="color: #008080;">$group</span>/<span class="nv" style="color: #008080;">$sample</span> <span class="nt" style="color: #000080;">-g</span> <span class="o" style="font-weight: 600;">||</span> error <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">LINENO</span><span class="k" style="font-weight: 600;">}</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span><span class="si" style="color: #d14;">)</span> <span class="s2" style="color: #d14;">"See </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/logs/plasmidID.log for more information.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">command:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">summary_report_pid.py -i </span><span class="nv" style="color: #008080;">$output_dir</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$group</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;"> -g"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1054
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<td class="diff-line-num new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1055
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<td class="diff-line-num new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1077
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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">YELLOW</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">ALL DONE WITH plasmidID</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NC</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Thank you for using plasmidID</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span></pre>
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