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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqsero2">Debian Med / seqsero2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/ec14d87450850bc025e0e9530967e398fa5e0b8f">ec14d874</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:17:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">seqsero is written in Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/eedefc9c90e44d795b5d1c6eeb3b5c6c4cd0cc51">eedefc9c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:19:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/906034167260e58401e0d9127fe66d787218ca8e">90603416</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:19:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/3444ba69d0fc201e247067b68f77690e8149690c">3444ba69</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:21:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.0.2'
Update to upstream version '1.0.2'
with Debian dir ffe83ac55473ba0d43f2a9010d0468dbd9b0ebf0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/49cc2f9d4f76a6a44f772ade3e1f4e6a9ca79b3a">49cc2f9d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:21:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/381f3e4b22984a69611aa9f5ef4f3b3cb288da1d">381f3e4b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:21:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/f6f24b90cdcb480374caa755b9f6a5f4e55fea12">f6f24b90</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:21:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/50871ba55b2ada8f50d3469e9ed6433670338bcb">50871ba5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:30:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Usei buildsystem=pybuild
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqsero2/commit/bea8e71b7fc2a8613b03d15e757bd584fedcc068">bea8e71b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-11T15:30:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup changelog from automatic changes
</pre>
</li>
</ul>
<h4>20 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#33896e6e3d46b21f0cca041ede579e6e4c464f2f">
<span class="deleted-file">
−
H_and_O_and_specific_genes.fasta
</span>
</a>
</li>
<li class="file-stats">
<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">
<span class="new-file">
+
MANIFEST.in
</span>
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#3e9acacf0e8150aa069145bd9c25fed4f38a70ea">
<span class="new-file">
+
__pycache__/Initial_Conditions.cpython-34.pyc
</span>
</a>
</li>
<li class="file-stats">
<a href="#0ad54d5d265a56f66fac141cbab8cd99ccda6078">
<span class="new-file">
+
__pycache__/version.cpython-34.pyc
</span>
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</li>
<li class="file-stats">
<a href="#353f485114641d0343bdd0a811f25fe0de4d9f03">
Initial_Conditions.py
→
bin/Initial_Conditions.py
</a>
</li>
<li class="file-stats">
<a href="#ea6bf378e28f298e24d57355422077c09f6c92cd">
SeqSero2_package.py
→
bin/SeqSero2_package.py
</a>
</li>
<li class="file-stats">
<a href="#b7c4327671510115c6fcc865032d0e9fef1c718b">
SeqSero2_update_kmer_database.py
→
bin/SeqSero2_update_kmer_database.py
</a>
</li>
<li class="file-stats">
<a href="#88716e4328181e8f99525646ed4a92e03d9661f6">
deinterleave_fastq.sh
→
bin/deinterleave_fastq.sh
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<li class="file-stats">
<a href="#8027f83a71b6358278b6bf0be04a8b7188dfc64b">
<span class="new-file">
+
seqsero2_db/H_and_O_and_specific_genes.fasta
</span>
</a>
</li>
<li class="file-stats">
<a href="#787186626ffc5d4caa57767f0bc18bf1cc6641f4">
antigens.pickle
→
seqsero2_db/antigens.pickle
</a>
</li>
<li class="file-stats">
<a href="#bc4f385db6d82f0fcb514281606f054f16305217">
invA_mers_dict
→
seqsero2_db/invA_mers_dict
</a>
</li>
<li class="file-stats">
<a href="#468dd2b4378046cc4d14ea51ad36846f59ab327e">
special.pickle
→
seqsero2_db/special.pickle
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
<span class="new-file">
+
setup.py
</span>
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</li>
<li class="file-stats">
<a href="#6defec8c57d89c1d5b6d02a6f7adc9f898c9b505">
<span class="new-file">
+
version.py
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="33896e6e3d46b21f0cca041ede579e6e4c464f2f">
<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#33896e6e3d46b21f0cca041ede579e6e4c464f2f"><strong>H_and_O_and_specific_genes.fasta</strong>
deleted
</a>
The diff for this file was not included because it is too large.
<br>
</li>
<li id="8875df48c18030126ef5ef5a6f5c93b23451fb9f">
<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#8875df48c18030126ef5ef5a6f5c93b23451fb9f"><strong>MANIFEST.in</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">include LICENSE</span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">include README.md</span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">include MANIFEST.in</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">include version.py</span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">include setup.py</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">include seqsero2_db/antigens.pickle</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">include seqsero2_db/H_and_O_and_specific_genes.fasta</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">include seqsero2_db/invA_mers_dict</span>
</pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">include seqsero2_db/special.pickle</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">include bin/deinterleave_fastq.sh</span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># SeqSero2 <span class="idiff left right">alpha-test version</span></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown">Salmonella serotyp<span class="idiff left right">ing from genome sequencing data</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># SeqSero2 <span class="idiff left right">v1.0.1</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown">Salmonella serotyp<span class="idiff left right">e prediction from genome sequencing data.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">Online version: http://www.denglab.info/SeqSero2</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gh" style="color: #999;"># Introduction </span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown">SeqSero2 is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies. This is a alpha test version. A web app will be available soon.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #999;"># Dependencies </span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">SeqSero has two modes:</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">SeqSero has three workflows:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">(A) <span class="idiff left">k-mer based mode (default), which applies unique k-mers of serotype determinant alleles to determine Salmonella serotypes in a fast speed. Special thanks to Dr. Hendrik Den Bakker for his significant contribution to this mode, details can be found in </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">SeqSeroK</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/hcdenbakker/SeqSeroK</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> and </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">SalmID</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/hcdenbakker/SalmID</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">.</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">(A) <span class="idiff left right">Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). </span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="idiff left right">K-mer mode is a independant pipeline, it only requires</span>:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="idiff left right">Allele micro-assembly workflow depends on</span>:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">1.</span> Python 3;</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p">2.</span> <span class="p">[</span><span class="nv" style="color: #008080;">SRA Toolkit</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">optional,</span> just used to fastq-dump sra files);</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">2.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Burrows-Wheeler Aligner v0.7.12</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sourceforge.net/projects/bio-bwa/files/</span><span class="p">)</span>;</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="idiff left right">(B) allele based mode (if users want to extract serotype determinant alleles), which applies a hybrid approach of reads-mapping and micro-assembly.</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p"><span class="idiff left">3.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Samtools v1.8</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://sourceforge.net/projects/samtools/files/samtools/</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="idiff left right">Allele mode depends on:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p"><span class="idiff left">4.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">NCBI BLAST v2.2.28+</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="p"><span class="idiff left">1.</span></span><span class="idiff right"> Python 3; </span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p"><span class="idiff left">5.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">SRA Toolkit v2.8.0</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="p"><span class="idiff left">2.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Burrows-Wheeler Aligner</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://sourceforge.net/projects/bio-bwa/files/</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">; </span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p"><span class="idiff left">6.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">SPAdes v3.9.0</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://bioinf.spbau.ru/spades</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"><span class="p"><span class="idiff left">3.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Samtools</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">http://sourceforge.net/projects/samtools/files/samtools</span>/</span><span class="p">)</span>;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="p"><span class="idiff left">7.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Bedtools v2.17.0</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">http://bedtools.readthedocs.io/en/latest</span>/</span><span class="p">)</span>;</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="p"><span class="idiff left">4.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">NCBI BLAST</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p"><span class="idiff left">8.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">SalmID v0.11</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/hcdenbakker/SalmID</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">.</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="p">5.</span> <span class="p">[</span><span class="nv" style="color: #008080;">SRA Toolkit</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software</span><span class="p">)</span>;</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="p">6.</span> <span class="p">[</span><span class="nv" style="color: #008080;">SPAdes</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bioinf.spbau.ru/spades</span><span class="p">)</span>;</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">(B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">Raw reads k-mer workflow (originally SeqSeroK) depends on:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">1.</span> Python 3;</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p">2.</span> <span class="p">[</span><span class="nv" style="color: #008080;">SRA Toolkit</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">optional,</span> just used to fastq-dump sra files);</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="p">7.</span> <span class="p">[</span><span class="nv" style="color: #008080;">Bedtools</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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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown"><span class="p"><span class="idiff left">8.</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">SalmID</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/hcdenbakker/SalmID</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">.</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="idiff left right">(C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"><span class="gh" style="color: #999;"># Executing the code </span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,7 +46,7 @@ Make sure all SeqSero2 and its dependency executables are added to your path (e.</td>
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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="sb" style="color: #d14;"> Usage: SeqSero2_package.py </span></span>
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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="LC47" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -m <string> (which <span class="idiff left right">mode to apply, 'k'(kmer mode), 'a'(allele mode), default=k</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -m <string> (which <span class="idiff left right">workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq)</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,23 +58,26 @@ Make sure all SeqSero2 and its dependency executables are added to your path (e.</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"> </span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"> -d <span class="nt" style="color: #000080;"><string></span> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number)</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown"> -c <span class="nt" style="color: #000080;"><flag></span> (if '-c' was flagged, SeqSero2 will use clean mode and only output serotyping prediction without the directory containing log files)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"> -c <span class="nt" style="color: #000080;"><flag></span> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files)</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"> --check <span class="nt" style="color: #000080;"><flag></span> (use '--check' flag to check the required dependencies)</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"> -v, --version (show program's version number and exit)</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"> </span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"><span class="gh" style="color: #999;"># Examples</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"><span class="idiff left right">K-mer</span> mode:</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="idiff left right">Allele</span> mode:</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"><span class="sb" style="color: #d14;"> # <span class="idiff left right">K-mer (default), for separated paired-end raw reads ("-t 2</span>")</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> SeqSero2_package.py</span> -t 2 -i R1.fastq.gz R2.fastq.gz</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="sb" style="color: #d14;"> # <span class="idiff left right">Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10</span>")</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> SeqSero2_package.py -p 10</span> -t 2 -i R1.fastq.gz R2.fastq.gz</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"><span class="sb" style="color: #d14;"> # K-mer (default), for assemblies ("-t 4", assembly only predcited by K-mer mode)</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown"><span class="sb" style="color: #d14;"> SeqSero2_package.py -t 4 -i assembly.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown">K-mer mode:</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown">Allele mode:</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="sb" style="color: #d14;"> # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2")</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="sb" style="color: #d14;"> SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="sb" style="color: #d14;"> # Allele mode ("-m a"), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10")</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown"><span class="sb" style="color: #d14;"> SeqSero2_package.py -m a -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="sb" style="color: #d14;"> # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k")</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="sb" style="color: #d14;"> SeqSero2_package.py -m k -t 4 -i assembly.fasta</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown"><span class="gh" style="color: #999;"># Output </span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown">Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'Seqsero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode).</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">@@ -11,20 +11,41 @@ import pickle</td>
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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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<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;">itertools</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">LooseVersion</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.spawn</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">find_executable</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" 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="LC17" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqSero2_version</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#ImportError</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;">version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqSero2_version</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="c1" style="color: #998; font-style: italic;">### SeqSero Kmer</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_args</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">"Parse the input arguments, use '-h' for help."</span></span>
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<pre style="margin: 0;">-<span id="LC18" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'SeqSero2_package.py -t <data_type> -m <mode> -i <input_data> [-<span class="idiff left">p <number of threads>] [-b <BWA_algorithm>]</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Developper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">Contact email:seqsero@gmail.com</span>'</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#add "-m <data_type>" in future</span></span>
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<pre style="margin: 0;">-<span id="LC19" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-i"</span><span class="p">,</span><span class="n" style="color: #333;">nargs</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<string>: path/to/input_data"</span><span class="p"><span class="idiff left right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-t"</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">,</span><span class="s" style="color: #d14;">'2'</span><span class="p">,</span><span class="s" style="color: #d14;">'3'</span><span class="p">,</span><span class="s" style="color: #d14;">'4'</span><span class="p">,</span><span class="s" style="color: #d14;">'5'</span><span class="p">,</span><span class="s" style="color: #d14;">'6'</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;">"<int>: '1'<span class="idiff left right">(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'sam'</span><span class="p">,</span><span class="s" style="color: #d14;">'mem'</span><span class="p">],</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"mem"</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;">"<string>: <span class="idiff left">mode for mapping, 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=mem"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-p"</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1"</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;">"<int>: <span class="idiff left">threads used for mapping mode, if p>4, only 4 threads will be used for assembly, default=1"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC23" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-m"</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'k'</span><span class="p">,</span><span class="s" style="color: #d14;">'a'</span><span class="p">],</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left">k"</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">help</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">"<string>: 'k'(kmer mode), 'a'(allele mode), default=k"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC24" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'SeqSero2_package.py -t <data_type> -m <mode> -i <input_data> [-<span class="idiff left">d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Developper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s" style="color: #d14;"><span class="idiff">Contact email:seqsero@gmail.com</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n</span></span><span class="s" style="color: #d14;"><span class="idiff right">Version: v1.0.2</span>'</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#add "-m <data_type>" in future</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-i"</span><span class="p">,</span><span class="n" style="color: #333;">nargs</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<string>: path/to/input_data"</span><span class="p"><span class="idiff left">,</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">type</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">abspath</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">### ed_SL_05282019: add 'type=os.path.abspath' to generate absolute path of input data.</span></span></span>
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<pre style="margin: 0;">+<span id="LC26" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-t"</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'1'</span><span class="p">,</span><span class="s" style="color: #d14;">'2'</span><span class="p">,</span><span class="s" style="color: #d14;">'3'</span><span class="p">,</span><span class="s" style="color: #d14;">'4'</span><span class="p">,</span><span class="s" style="color: #d14;">'5'</span><span class="p">,</span><span class="s" style="color: #d14;">'6'</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;">"<int>: '1'<span class="idiff left right"> for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'sam'</span><span class="p">,</span><span class="s" style="color: #d14;">'mem'</span><span class="p">],</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"mem"</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;">"<string>: <span class="idiff left">algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC28" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-p"</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1"</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;">"<int>: <span class="idiff left">number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC29" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-m"</span><span class="p">,</span><span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'k'</span><span class="p">,</span><span class="s" style="color: #d14;">'a'</span><span class="p">],</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left">a"</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">help</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">"<string>: which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC30" 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;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-d"</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;">"<string>: output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-c"</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;">"<flag>: if '-c' was flagged, SeqSero2 will use clean mode and only output serotyping prediction, the directory containing log files will be deleted"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-c"</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;">"<flag>: if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--check"</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;">"<flag>: use '--check' flag to check the required dependencies"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--version'</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;">'version'</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%(prog)</span><span class="s" style="color: #d14;">s '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SeqSero2_version</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</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="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">### ed_SL_05282019: check paths of dependencies</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="n" style="color: #333;">check_dependencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_args</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">dependencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'bwa'</span><span class="p">,</span><span class="s" style="color: #d14;">'samtools'</span><span class="p">,</span><span class="s" style="color: #d14;">'blastn'</span><span class="p">,</span><span class="s" style="color: #d14;">'fastq-dump'</span><span class="p">,</span><span class="s" style="color: #d14;">'spades.py'</span><span class="p">,</span><span class="s" style="color: #d14;">'bedtools'</span><span class="p">,</span><span class="s" style="color: #d14;">'SalmID.py'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">check_dependencies</span><span class="p">:</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">item</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dependencies</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="python"> <span class="n" style="color: #333;">ext_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_executable</span><span class="p">(</span><span class="n" style="color: #333;">item</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext_path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="p">(</span><span class="s" style="color: #d14;">"Using "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">item</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;">ext_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" 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="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="p">(</span><span class="s" style="color: #d14;">"ERROR: can not find "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">item</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" in PATH"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">### end of --check</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">complement</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">'A'</span><span class="p">:</span> <span class="s" style="color: #d14;">'T'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -258,11 +279,9 @@ def Combine(b, c):</td>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">seqsero_from_formula_to_serotypes</span><span class="p">(</span><span class="n" style="color: #333;">Otype</span><span class="p">,</span> <span class="n" style="color: #333;">fliC</span><span class="p">,</span> <span class="n" style="color: #333;">fljB</span><span class="p">,</span> <span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">subspecies</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#like test_output_06012017.txt</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list)</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Initial_Conditions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">phase1</span></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Initial_Conditions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">phase2</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Initial_Conditions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">phaseO</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Initial_Conditions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">sero</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Initial_Conditions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">subs</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Initial_Conditions</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">phase1</span><span class="p">,</span><span class="n" style="color: #333;">phase2</span><span class="p">,</span><span class="n" style="color: #333;">phaseO</span><span class="p">,</span><span class="n" style="color: #333;">sero</span><span class="p">,</span><span class="n" style="color: #333;">subs</span><span class="p">,</span><span class="n" style="color: #333;">remove_list</span><span class="p">,</span><span class="n" style="color: #333;">rename_dict</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">rename_dict_not_anymore</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">rename_dict</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rename_dict</span><span class="p">]</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="n" style="color: #333;">rename_dict_all</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rename_dict_not_anymore</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;">rename_dict</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#used for decide whether to </span></span>
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266
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">seronames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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267
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">seronames_none_subspecies</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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268
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">phase1</span><span class="p">)):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="339" 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">@@ -320,9 +339,20 @@ def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subsp</td>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">new_fliC</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fliC_combine</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">fliC</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fliC_combine</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">new_fljB</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fljB_combine</span></span>
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322
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">fljB</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fljB_combine</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;">if</span> <span class="n" style="color: #333;">subs</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;">subspecies</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">seronames</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">sero</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">seronames_none_subspecies</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">sero</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">######start, remove_list,rename_dict, added on 11/11/2018</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sero</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">remove_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">temp_sero</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sero</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">temp_sero</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rename_dict</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;">temp_sero</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">rename_dict</span><span class="p">[</span><span class="n" style="color: #333;">temp_sero</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;">#rename if in the rename list</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">temp_sero</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;">seronames</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">#the new sero may already included, if yes, then not consider</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subs</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;">subspecies</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">seronames</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">temp_sero</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">seronames_none_subspecies</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">temp_sero</span><span class="p">)</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" 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="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC353" 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="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">######end, added on 11/11/2018</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#analyze seronames</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;">subspecies_pointer</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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328
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seronames</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seronames_none_subspecies</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 unfold js-unfold new_line" data-linenumber="366" 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">@@ -336,10 +366,12 @@ def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subsp</td>
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336
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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;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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337
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<td class="diff-line-num new_line" data-linenumber="367" 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">
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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seronames</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="c1" style="color: #998; font-style: italic;">#there are two possible predictions for serotypes</span></span>
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338
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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;">star</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*"</span></span>
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339
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<td class="diff-line-num new_line old" data-linenumber="369" 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="LC339" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"The predicted serotypes share the same general formula:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Otype</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;">fliC</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;">fljB</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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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#changed 04072019</span></span>
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<td class="diff-line-num new new_line" data-linenumber="370" 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">
370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n"</span></span>
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340
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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;">if</span> <span class="n" style="color: #333;">subspecies_pointer</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"1"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seronames_none_subspecies</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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341
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">star</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"*"</span></span>
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342
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<td class="diff-line-num new_line old" data-linenumber="373" 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="LC342" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span></span>
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<td class="diff-line-num new new_line" data-linenumber="373" 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">
373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" The predicted O and H antigens correspond to serotype '"</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="s" style="color: #d14;">" or "</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">seronames</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">star_line</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line</span></span>
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343
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Otype</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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344
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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;">Otype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"-"</span></span>
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345
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">predict_form</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Otype</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;">fliC</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;">fljB</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="350" 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="382" 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">@@ -350,23 +382,30 @@ def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subsp</td>
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350
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">special_gene_list</span><span class="p">:</span></span>
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351
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"sdf"</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">sdf</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="LC353" class="line" lang="python"> <span class="n" style="color: #333;">predict_form</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_form</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" Sdf prediction:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sdf</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"</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;">star_line</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" sdf gene detected."</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: new output format</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#predict_form = predict_form + " Sdf prediction:" + sdf</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;">predict_form</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_form</span> <span class="c1" style="color: #998; font-style: italic;">#changed 04072019</span></span>
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354
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sdf</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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355
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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;">star</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*"</span></span>
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356
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<td class="diff-line-num new_line old" data-linenumber="391" 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="LC356" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gallinarum/Enteritidis sdf -"</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" sdf gene not detected."</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: new output format</span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#changed in 04072019, for new output</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n"</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Gallinarum or Enteritidis"</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: new output format</span></span>
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358
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">###end of special test for Enteritidis</span></span>
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359
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">predict_form</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"4:i:-"</span><span class="p">:</span></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">potential monophasic variant of Typhimurium"</span></span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left">I 4,[5],12:i:-"</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># ed_SL_09242019: change serotype name</span></span></span>
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361
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">predict_form</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"4:r:-"</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;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">potential monophasic variant of Heidelberg</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">predict_form</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"4:b:-"</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;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">potential monophasic variant of Paratyphi B</span>"</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;"><span class="idiff left">elif</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">predict_form</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"8:e,h:1,2"</span></span><span class="p"><span class="idiff right">:</span></span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Newport"</span></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">star</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*"</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;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."</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;">claim</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. </span> New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">4:r:-</span>"</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">predict_form</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"4:b:-"</span><span class="p">:</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># ed_SL_09272019: change for new output format</span></span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">N/A (4:b:-)</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo</span></span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>predict_sero = "Newport"</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>star = "*"</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">claim</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right"> The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme.</span> New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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370
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"N/A"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">predict_sero</span><span class="p">:</span></span>
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371
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">claim</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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372
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#special test for Typhimurium</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="420" 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">@@ -381,9 +420,11 @@ def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subsp</td>
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381
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">normal</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mutation</span><span class="p">:</span></span>
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382
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">normal</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mutation</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"(O5-)"</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;">#predict_sero = predict_sero.strip() + "(O5-)"</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;">#diable special sero for new output requirement, 04132019</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC386" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Detected the deletion of O5-."</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line = "Detected the deletion of O5-."</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" Detected a deletion that causes O5- variant of Typhimurium."</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: new output format</span></span>
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<pre style="margin: 0;"> <span id="LC428" 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="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#special test for Paratyphi B</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="397" 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">@@ -397,23 +438,29 @@ def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subsp</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">mutation</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;">special_gene_list</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(normal,mutation)</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">normal</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mutation</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"(dt+)"</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">' var. L(+) tartrate+'</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"Paratyphi B"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">predict_sero</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: new output format</span></span>
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401
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC402" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)."</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)."</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. "</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: new output format</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">normal</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mutation</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"(dt-)"</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</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;">star</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"*"</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;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B."</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B."</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B."</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: new output format</span></span>
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407
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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408
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC409" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not."</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not."</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span> <span class="c1" style="color: #998; font-style: italic;">## ed_SL_05152019: do not report this situation.</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#special test for O13,22 and O13,23</span></span>
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411
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">Otype</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"13"</span><span class="p">:</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">ex_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#ex_dir = os.path.dirname(os.path.realpath(__file__))</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">ex_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)),</span><span class="s" style="color: #d14;">'seqsero2_db'</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_09152019</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">ex_dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/special.pickle'</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">special</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pickle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">O22_O23</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">special</span><span class="p">[</span><span class="s" style="color: #d14;">'O22_O23'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" or "</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">O22_O23</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 class="idiff left right">:</span></span></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;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" or "</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">O22_O23</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="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">predict_sero</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">" or "</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rename_dict_all</span></span><span class="p"><span class="idiff">:</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#if in rename_dict_all, then it means already merged, no need to analyze </span></span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"> <span class="n" style="color: #333;">O22_score</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="LC465" class="line" lang="python"> <span class="n" style="color: #333;">O23_score</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="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">special_gene_list</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -426,26 +473,28 @@ def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subsp</td>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" or "</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">z</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">O22_score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">O23_score</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC429" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">star_line</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Detected O22 specific genes to further differenciate '"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">predict_sero</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"'."</span></span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019</span></span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z</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="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">O22_score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">O23_score</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC433" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">star_line</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Detected O23 specific genes to further differenciate '"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">predict_sero</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"'."</span></span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019</span></span></span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z</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="LC482" 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="LC483" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC437" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Fail to detect O22 and O23 differences."</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">" or "</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">predict_sero</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" The predicted serotypes share the same general formula:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Otype</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;">fliC</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;">fljB</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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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#special test for O6,8 </span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">merge_O68_list</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"Blockley"</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff">"Bovismorbificans"</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff">"Hadar"</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff">"Litchfield"</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff">"Manhattan"</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff">"Muenchen"</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">merge_O68_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">predict_sero</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC444" class="line" lang="python"> <span class="n" style="color: #333;">star_line</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="LC488" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list</span></span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>for x in merge_O68_list:</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> if x in predict_sero:</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> predict_sero=x</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> star=""</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> star_line=""</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#special test for Montevideo; most of them are monophasic</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Montevideo"</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">predict_sero</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"1,2,7"</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">predict_form</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">star</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="LC448" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination."</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list</span></span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>star="*"</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination."</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">predict_form</span><span class="p">,</span> <span class="n" style="color: #333;">predict_sero</span><span class="p">,</span> <span class="n" style="color: #333;">star</span><span class="p">,</span> <span class="n" style="color: #333;">star_line</span><span class="p">,</span> <span class="n" style="color: #333;">claim</span></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">### End of SeqSero Kmer part</span></span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -643,21 +692,26 @@ def decide_O_type_and_get_special_genes(Final_list,Final_list_passed):</td>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">potenial_new_gene</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="LC693" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"two differnt genes in same contig, fix it for O antigen"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">potenial_new_gene</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="LC646" class="line" lang="python"> <span class="n" style="color: #333;">final_O</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">potenial_new_gene</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python"> <span class="n" style="color: #333;">pointer</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="LC696" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">final_O</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">y</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;">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="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">potenial_new_gene</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;">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="LC698" class="line" lang="python"> <span class="n" style="color: #333;">pointer</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="LC699" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pointer</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#changed to consider two genes in same contig</span></span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="python"> <span class="n" style="color: #333;">final_O</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">potenial_new_gene</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### end of the two genes on same contig test</span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="python"> <span class="n" style="color: #333;">final_O</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">final_O</span><span class="p">,</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#sorted</span></span>
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703
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<pre style="margin: 0;"> <span id="LC703" 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;">final_O</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">final_O</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"O-1,3,19_not_in_3,10"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">final_O</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]):</span></span>
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650
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print "$$$No Otype, due to no hit"#may need to be changed</span></span>
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651
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"-"</span></span>
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652
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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653
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"> <span class="n" style="color: #333;">highest_O_coverage</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">final_O</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"O-1,3,19_not_in_3,10"</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]])</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">highest_O_coverage</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">final_O</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"O-1,3,19_not_in_3,10"</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]])</span></span>
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"> <span class="n" style="color: #333;">O_list</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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655
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"> <span class="n" style="color: #333;">O_list_less_contamination</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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656
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">final_O</span><span class="p">:</span></span>
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657
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="s" style="color: #d14;">"O-1,3,19_not_in_3,10__130"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span><span class="c1" style="color: #998; font-style: italic;">#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off</span></span>
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658
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"> <span class="n" style="color: #333;">O_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"__"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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659
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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"> <span class="n" style="color: #333;">O_nodes_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"___"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_O_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.15</span><span class="p">:</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_O_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.15</span><span class="p">:</span></span>
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661
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"> <span class="n" style="color: #333;">O_list_less_contamination</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"__"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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662
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### special test for O9,46 and O3,10 family</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="s" style="color: #d14;">"O-9,46_wbaV"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">O_list</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">O_list</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">O_list_less_contamination</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;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"O-9,"</span><span class="p">):</span><span class="c1" style="color: #998; font-style: italic;">#not sure should use and float(O9_wbaV)/float(num_1) > 0.1</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">@@ -695,7 +749,7 @@ def decide_O_type_and_get_special_genes(Final_list,Final_list_passed):</td>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span> </span>
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696
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="python"> <span class="n" style="color: #333;">max_score</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span></span>
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">final_O</span><span class="p">:</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</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;">max_score</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_O_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.15</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</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;">max_score</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_O_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.15</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold</span></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="python"> <span class="n" style="color: #333;">max_score</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">#change from x[-1] to x[2],08172018</span></span>
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700
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"O-1,3,19"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="726" 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">@@ -726,7 +780,7 @@ def decide_O_type_and_get_special_genes(Final_list,Final_list_passed):</td>
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="python"> <span class="n" style="color: #333;">contamination_O</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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781
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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728
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python"> <span class="n" style="color: #333;">contamination_O</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"potential contamination from O antigen signals"</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">O_nodes_list</span><span class="p">,</span><span class="n" style="color: #333;">special_genes</span><span class="p">,</span><span class="n" style="color: #333;">final_O</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">O_nodes_list</span><span class="p">,</span><span class="n" style="color: #333;">special_genes</span><span class="p">,</span><span class="n" style="color: #333;">final_O</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">Otypes_uniq</span></span></span>
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">### End of SeqSero2 allele prediction and output</span></span>
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="python"></span>
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_input_files</span><span class="p">(</span><span class="n" style="color: #333;">make_dir</span><span class="p">,</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span><span class="n" style="color: #333;">data_type</span><span class="p">,</span><span class="n" style="color: #333;">dirpath</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -764,41 +818,60 @@ def get_input_files(make_dir,input_file,data_type,dirpath):</td>
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="s" style="color: #d14;">".."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">for_fq</span><span class="p">,</span><span class="n" style="color: #333;">rev_fq</span></span>
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">predict_O_and_H_types</span><span class="p">(</span><span class="n" style="color: #333;">Final_list</span><span class="p">,</span><span class="n" style="color: #333;">Final_list_passed</span><span class="p">):</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">predict_O_and_H_types</span><span class="p">(</span><span class="n" style="color: #333;">Final_list</span><span class="p">,</span><span class="n" style="color: #333;">Final_list_passed</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">new_fasta</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#get O and H types from Final_list from blast parsing; allele mode</span></span>
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<pre style="margin: 0;">+<span id="LC823" 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="LC824" class="line" lang="python"> <span class="n" style="color: #333;">fliC_choice</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="LC825" class="line" lang="python"> <span class="n" style="color: #333;">fljB_choice</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="LC826" class="line" lang="python"> <span class="n" style="color: #333;">fliC_contig</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NA"</span></span>
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"> <span class="n" style="color: #333;">fljB_contig</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NA"</span></span>
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"> <span class="n" style="color: #333;">fliC_region</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">set</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="LC829" class="line" lang="python"> <span class="n" style="color: #333;">fljB_region</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">set</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="LC775" class="line" lang="python"> <span class="n" style="color: #333;">fliC_length</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;">#can be changed to coverage in future</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="python"> <span class="n" style="color: #333;">fljB_length</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;">#can be changed to coverage in future</span></span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">fliC_length</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;">#can be changed to coverage in future<span class="idiff left right">; in 03292019, changed to ailgned length</span></span></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="python"> <span class="n" style="color: #333;">fljB_length</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;">#can be changed to coverage in future<span class="idiff left right">; in 03292019, changed to ailgned length</span></span></span>
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"-"</span><span class="c1" style="color: #998; font-style: italic;">#no need to decide O contig for now, should be only one</span></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">O_nodes</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">O_nodes_roles</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">decide_O_type_and_get_special_genes</span><span class="p">(</span><span class="n" style="color: #333;">Final_list</span><span class="p">,</span><span class="n" style="color: #333;">Final_list_passed</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#decide the O antigen type and also return special-gene-list for further identification</span></span>
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">O_nodes</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">O_nodes_roles</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">Otypes_uniq</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">decide_O_type_and_get_special_genes</span><span class="p">(</span><span class="n" style="color: #333;">Final_list</span><span class="p">,</span><span class="n" style="color: #333;">Final_list_passed</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#decide the O antigen type and also return special-gene-list for further identification</span></span>
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779
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</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;">strip</span><span class="p">()</span></span>
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780
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"1,3,19"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">O_nodes_roles</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"1,3,19"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">O_nodes_roles</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">O_choice</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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781
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"-"</span></span>
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782
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="python"> <span class="n" style="color: #333;">H_contig_roles</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">decide_contig_roles_for_H_antigen</span><span class="p">(</span><span class="n" style="color: #333;">Final_list</span><span class="p">,</span><span class="n" style="color: #333;">Final_list_passed</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#decide the H antigen contig is fliC or fljB</span></span>
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<td class="diff-line-num new old_line" data-linenumber="783" 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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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#add alignment locations, used for further selection, 03312019</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">H_contig_roles</span><span class="p">)):</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">H_contig_roles</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Final_list_passed</span><span class="p">:</span></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">y</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;">startswith</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]):</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="python"> <span class="n" style="color: #333;">H_contig_roles</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;">H_contig_roles</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="p">(</span><span class="n" style="color: #333;">y</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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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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783
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"SeqSero_log.txt"</span><span class="p">,</span><span class="s" style="color: #d14;">"a"</span><span class="p">)</span></span>
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784
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"O_contigs:"</span><span class="p">)</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python"> <span class="n" style="color: #333;">extract_file</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"Extracted_antigen_alleles.fasta"</span><span class="p">,</span><span class="s" style="color: #d14;">"a"</span><span class="p">)</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="python"> <span class="n" style="color: #333;">handle_fasta</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;">SeqIO</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">new_fasta</span><span class="p">,</span><span class="s" style="color: #d14;">"fasta"</span><span class="p">))</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python"></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("O_contigs:")</span></span>
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785
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"O_contigs:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python"> <span class="n" style="color: #333;">extract_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="852" 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">
852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="python"> <span class="n" style="color: #333;">extract_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#O_contigs:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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786
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<td class="diff-line-num new_line" data-linenumber="853" 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">
853
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">O_nodes_roles</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="787" 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">
787
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<td class="diff-line-num new_line" data-linenumber="854" 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">
854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"O-1,3,19_not_in_3,10"</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span><span class="c1" style="color: #998; font-style: italic;">#O-1,3,19_not_in_3,10 is just a small size marker</span></span>
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788
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<td class="diff-line-num new_line old" data-linenumber="855" 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="LC788" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">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;">x</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;">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="s" style="color: #d14;">"blast score:"</span><span class="p">,</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"identity</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">:"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">x</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">x</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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789
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<td class="diff-line-num new_line old" data-linenumber="855" 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="LC789" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">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="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;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"__"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"blast score: "</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"identity</span><span class="si" style="color: #d14;">%</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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">x</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">% </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="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1])))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="856" 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">
856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">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="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;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"__"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"; "</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"blast score: "</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" identity</span><span class="si" style="color: #d14;">%</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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">x</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">; alignment from "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" of antigen</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">title</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;">x</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;">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="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;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"__"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"; "</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"blast score: "</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" identity</span><span class="si" style="color: #d14;">%</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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">x</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">; alignment from "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">x</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" of antigen</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> </span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">z</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handle_fasta</span><span class="p">:</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</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;">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="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description</span><span class="p">:</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">seqs</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;">z</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">extract_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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790
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863
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<pre style="margin: 0;"> <span id="LC863" 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;">H_contig_roles</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 old_line" data-linenumber="791" 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">
791
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="python"> <span class="n" style="color: #333;">highest_H_coverage</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">H_contig_roles</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;">#less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">highest_H_coverage</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">([</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">H_contig_roles</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;">#less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output</span></span>
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792
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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793
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="python"> <span class="n" style="color: #333;">highest_H_coverage</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span></span>
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794
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">H_contig_roles</span><span class="p">:</span></span>
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795
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if multiple choices, temporately select the one with longest length for now, will revise in further change</span></span>
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796
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"fliC"</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="n" style="color: #333;"><span class="idiff">fliC_length</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">O_nodes</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_cov_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_H_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.13</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">#remember to avoid the effect of O-type contig, so should not in O_node list</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"fliC"</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="n" style="color: #333;"><span class="idiff">fliC_length</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">O_nodes</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_cov_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_H_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.13</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">#remember to avoid the effect of O-type contig, so should not in O_node list</span></span>
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="n" style="color: #333;">fliC_contig</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</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="LC798" class="line" lang="python"> <span class="n" style="color: #333;">fliC_length</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC799" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"fljB"</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="n" style="color: #333;"><span class="idiff">fljB_length</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">O_nodes</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_cov_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_H_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.13</span><span class="p">:</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="python"> <span class="n" style="color: #333;">fliC_length</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">])</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"fljB"</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="n" style="color: #333;"><span class="idiff">fljB_length</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">O_nodes</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_cov_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">highest_H_coverage</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.13</span><span class="p">:</span></span>
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="python"> <span class="n" style="color: #333;">fljB_contig</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</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="LC801" class="line" lang="python"> <span class="n" style="color: #333;">fljB_length</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff right">3</span></span><span class="p">])</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="python"> <span class="n" style="color: #333;">fljB_length</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">])</span></span>
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802
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Final_list_passed</span><span class="p">:</span></span>
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803
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fliC_choice</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"fliC_"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fliC_contig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>
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804
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"> <span class="n" style="color: #333;">fliC_choice</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="858" 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="931" 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">@@ -858,8 +931,9 @@ def predict_O_and_H_types(Final_list,Final_list_passed):</td>
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858
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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859
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932
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5)</span></span>
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860
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#end of removing none-middle contigs</span></span>
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861
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"H_contigs:"</span><span class="p">)</span></span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>print("H_contigs:")</span></span>
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862
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"H_contigs:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="python"> <span class="n" style="color: #333;">extract_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#H_contigs:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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863
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937
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<pre style="margin: 0;"> <span id="LC937" class="line" lang="python"> <span class="n" style="color: #333;">H_contig_stat</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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864
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="python"> <span class="n" style="color: #333;">H1_cont_stat</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>
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865
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939
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<pre style="margin: 0;"> <span id="LC939" class="line" lang="python"> <span class="n" style="color: #333;">H2_cont_stat</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="871" 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="945" 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">@@ -871,13 +945,25 @@ def predict_O_and_H_types(Final_list,Final_list_passed):</td>
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871
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945
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<pre style="margin: 0;"> <span id="LC945" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"first"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"last"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span> <span class="c1" style="color: #998; font-style: italic;">#this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide</span></span>
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872
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946
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Final_list_passed</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#it's impossible to has the "first" and "last" allele as prediction, so re-do it</span></span>
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873
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span><span class="c1" style="color: #998; font-style: italic;">#it's very possible to be third phase allele, so no need to make it must be fliC or fljB</span></span>
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874
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"can't_decide_fliC_or_fljB"</span><span class="p">,</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"blast_score:"</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"identity</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">:"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">y</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">y</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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875
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"<span class="idiff left"> "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"blast_score: "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">" identity</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">:"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">round</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">% </span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">min</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">" to "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">max</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1])))</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"<span class="idiff left">; "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"blast score: "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">" identity</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">: "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">round</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">; alignment from "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">min</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">" to "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">max</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]))</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">" of antigen</span></span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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876
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950
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<pre style="margin: 0;"> <span id="LC950" class="line" lang="python"> <span class="n" style="color: #333;">H_contig_roles</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"can't decide fliC or fljB, may be third phase"</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="python"> <span class="n" style="color: #333;">title</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span 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;">"blast score: "</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;">y</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" identity</span><span class="si" style="color: #d14;">%</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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">y</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">; alignment from "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" of antiten</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">z</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handle_fasta</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="954" 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">
954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</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;">z</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description</span><span class="p">:</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="python"> <span class="n" style="color: #333;">seqs</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;">z</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="python"> <span class="n" style="color: #333;">extract_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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877
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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878
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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879
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"blast_score:"</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"identity</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">:"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">y</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">y</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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880
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span 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;">"blast_score: "</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;">y</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" identity</span><span class="si" style="color: #d14;">%</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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">y</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">% </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="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1])))</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span 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;">"blast score: "</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;">y</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" identity</span><span class="si" style="color: #d14;">%</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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">y</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">; alignment from "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" of antigen</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="python"> <span class="n" style="color: #333;">title</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;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span 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;">"blast score: "</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;">y</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" identity</span><span class="si" style="color: #d14;">%</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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">y</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="mi" style="color: #099;">100</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">; alignment from "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" to "</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">y</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="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" of antigen</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="963" 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">
963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">z</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handle_fasta</span><span class="p">:</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</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;">z</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">description</span><span class="p">:</span></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="python"> <span class="n" style="color: #333;">seqs</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;">z</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="python"> <span class="n" style="color: #333;">extract_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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881
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"fliC"</span><span class="p">:</span></span>
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882
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">H1_cont_stat</span><span class="p">:</span></span>
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883
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969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="python"> <span class="n" style="color: #333;">H1_cont_stat</span><span class="p">[</span><span class="n" style="color: #333;">y</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="899" 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">@@ -899,12 +985,41 @@ def predict_O_and_H_types(Final_list,Final_list_passed):</td>
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899
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985
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<pre style="margin: 0;"> <span id="LC985" class="line" lang="python"> <span class="n" style="color: #333;">contamination_H</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"potential contamination from H antigen signals"</span></span>
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900
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986
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<pre style="margin: 0;"> <span id="LC986" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">H2_cont_stat_list</span><span class="p">)</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fljB_contig</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"NA"</span><span class="p">:</span></span>
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901
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987
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<pre style="margin: 0;"> <span id="LC987" class="line" lang="python"> <span class="n" style="color: #333;">contamination_H</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"potential contamination from H antigen signals, uncommon weak fljB signals detected"</span></span>
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902
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">contamination_O</span><span class="p">)</span></span>
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903
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">contamination_H</span><span class="p">)</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#get additional antigens</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="python"><span class="s" style="color: #d14;"> if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="python"><span class="s" style="color: #d14;"> if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1</span></span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="python"><span class="s" style="color: #d14;"> O_choice="O-9,46"</span></span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="python"><span class="s" style="color: #d14;"> #print "$$$Most possilble Otype: O-9,46"</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="python"><span class="s" style="color: #d14;"> elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="python"><span class="s" style="color: #d14;"> O_choice="O-9,46,27"</span></span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="python"><span class="s" style="color: #d14;"> #print "$$$Most possilble Otype: O-9,46,27"</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="python"><span class="s" style="color: #d14;"> elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="python"><span class="s" style="color: #d14;"> if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1</span></span>
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="python"><span class="s" style="color: #d14;"> O_choice="O-3,10"</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="python"><span class="s" style="color: #d14;"> #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="python"><span class="s" style="color: #d14;"> else:</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="python"><span class="s" style="color: #d14;"> O_choice="O-1,3,19"</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="python"><span class="s" style="color: #d14;"> #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="python"><span class="s" style="color: #d14;"> ### end of special test for O9,46 and O3,10 family</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="python"></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="python"><span class="s" style="color: #d14;"> if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19":</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="python"><span class="s" style="color: #d14;"> if len(Otypes_uniq)>2:</span></span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="python"><span class="s" style="color: #d14;"> contamination_O="potential contamination from O antigen signals"</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="python"><span class="s" style="color: #d14;"> else:</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="python"><span class="s" style="color: #d14;"> if len(Otypes_uniq)>1:</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="python"><span class="s" style="color: #d14;"> if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund</span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="python"><span class="s" style="color: #d14;"> contamination_O=""</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="python"><span class="s" style="color: #d14;"> elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="python"><span class="s" style="color: #d14;"> contamination_O=""</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="python"> <span class="n" style="color: #333;">additonal_antigents</span><span class="o" style="font-weight: 600;">=</span><span class="p">[]</span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(contamination_O)</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print(contamination_H)</span></span>
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904
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">contamination_O</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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905
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">contamination_H</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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906
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1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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907
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">fliC_choice</span><span class="p">,</span><span class="n" style="color: #333;">fljB_choice</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="p">,</span><span class="n" style="color: #333;">contamination_H</span></span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">fliC_choice</span><span class="p">,</span><span class="n" style="color: #333;">fljB_choice</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="p">,</span><span class="n" style="color: #333;">contamination_H</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">Otypes_uniq</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">H1_cont_stat_list</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">H2_cont_stat_list</span></span></span>
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908
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="python"></span>
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909
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_input_K</span><span class="p">(</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span><span class="n" style="color: #333;">lib_dict</span><span class="p">,</span><span class="n" style="color: #333;">data_type</span><span class="p">,</span><span class="n" style="color: #333;">k_size</span><span class="p">):</span></span>
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910
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#kmer mode; get input_Ks from dict and data_type</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1064" 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="1179" 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">@@ -1064,6 +1179,8 @@ def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_b</td>
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1064
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_mapped_reads_and_do_assembly_and_blast</span><span class="p">(</span><span class="n" style="color: #333;">current_time</span><span class="p">,</span><span class="n" style="color: #333;">sorted_bam</span><span class="p">,</span><span class="n" style="color: #333;">combined_fq</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq1</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq2</span><span class="p">,</span><span class="n" style="color: #333;">threads</span><span class="p">,</span><span class="n" style="color: #333;">fnameA</span><span class="p">,</span><span class="n" style="color: #333;">fnameB</span><span class="p">,</span><span class="n" style="color: #333;">database</span><span class="p">,</span><span class="n" style="color: #333;">mapping_mode</span><span class="p">):</span></span>
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1065
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#seqsero2 -a; extract, assembly and blast</span></span>
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1066
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<td class="diff-line-num new_line" data-linenumber="1181" 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">
1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"bamToFastq -i "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sorted_bam</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -fq "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">combined_fq</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("fnameA:",fnameA)</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("fnameB:",fnameB)</span></span>
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1067
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fnameB</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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1068
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"bamToFastq -i "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sorted_bam</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -fq "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mapped_fq1</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -fq2 "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mapped_fq2</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" 2>> data_log.txt"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#2> /dev/null if want no output</span></span>
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1069
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1074" 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="1191" 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">@@ -1074,12 +1191,13 @@ def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combi</td>
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1074
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1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"4"</span></span>
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1075
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1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1076
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<td class="diff-line-num new_line" data-linenumber="1193" 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">
1193
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<pre style="margin: 0;"> <span id="LC1193" class="line" lang="python"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threads</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1077" 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">
1077
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<td class="diff-line-num new_line old" data-linenumber="1194" 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="LC1077" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="n" style="color: #333;">combined_fq</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getsize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mapped_fq1</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff right">100</span></span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">#if not, then it's "-:-:-"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1194" 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">
1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="n" style="color: #333;">combined_fq</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fnameB</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getsize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">mapped_fq1</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff">100</span></span><span class="p"><span class="idiff right">)</span>:</span><span class="c1" style="color: #998; font-style: italic;">#if not, then it's "-:-:-"</span></span>
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1078
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1195
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<pre style="margin: 0;"> <span id="LC1195" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fnameB</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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1079
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1196
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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"spades.py --careful --pe1-s "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">combined_fq</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" --pe1-1 "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mapped_fq1</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" --pe1-2 "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mapped_fq2</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -t "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -o "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outdir</span><span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" >> data_log.txt 2>&1"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1080
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1197
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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1081
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"spades.py --careful --pe1-s "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">combined_fq</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -t "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -o "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outdir</span><span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" >> data_log.txt 2>&1"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1082
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<td class="diff-line-num new_line old" data-linenumber="1199" 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="LC1082" class="line" lang="python"> <span class="n" style="color: #333;">new_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnameA</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;">database</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;">mapping_mode</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".fasta"</span></span>
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1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta"</span></span>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="python"> <span class="n" style="color: #333;">new_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fnameA</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;">database</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'/'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">mapping_mode</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".fasta"</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_09152019: change path to databse for packaging</span></span>
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1083
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1201
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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"mv "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outdir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/contigs.fasta "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">new_fasta</span><span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" 2> /dev/null"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1084
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<td class="diff-line-num new_line" data-linenumber="1202" 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">
1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta</span></span>
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1085
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<td class="diff-line-num new_line" data-linenumber="1203" 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">
1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"rm -rf "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">outdir</span><span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" 2> /dev/null"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1089" 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="1207" 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">@@ -1089,7 +1207,7 @@ def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combi</td>
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1089
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<td class="diff-line-num new_line" data-linenumber="1207" 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">
1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"blastn -query "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">database</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -db "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">new_fasta</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"_db -out "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">xmlfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" -outfmt 5 >> data_log.txt 2>&1"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">###1/27/2015; 08272018, remove "-word_size 10"</span></span>
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1090
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<td class="diff-line-num new_line" data-linenumber="1208" 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">
1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1091
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<td class="diff-line-num new_line" data-linenumber="1209" 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">
1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="python"> <span class="n" style="color: #333;">xmlfile</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NA"</span></span>
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1092
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<td class="diff-line-num new_line old" data-linenumber="1210" 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="LC1092" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xmlfile</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1093" 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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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xmlfile</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">new_fasta</span></span></span>
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1093
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1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="python"></span>
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1094
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">judge_subspecies</span><span class="p">(</span><span class="n" style="color: #333;">fnameA</span><span class="p">):</span></span>
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1095
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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#seqsero2 -a; judge subspecies on just forward raw reads fastq</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1139" 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="1257" 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">@@ -1139,8 +1257,12 @@ def main():</td>
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1139
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1257
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<pre style="margin: 0;"> <span id="LC1257" class="line" lang="python"> <span class="n" style="color: #333;">make_dir</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">d</span></span>
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1140
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1258
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<pre style="margin: 0;"> <span id="LC1258" class="line" lang="python"> <span class="n" style="color: #333;">clean_mode</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">c</span></span>
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1141
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1259
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<pre style="margin: 0;"> <span id="LC1259" class="line" lang="python"> <span class="n" style="color: #333;">k_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">27</span> <span class="c1" style="color: #998; font-style: italic;">#will change for bug fixing</span></span>
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1142
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<pre style="margin: 0;">-<span id="LC1142" class="line" lang="python"> <span class="n" style="color: #333;">database</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"H_and_O_and_specific_genes.fasta"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1143" 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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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>database="H_and_O_and_specific_genes.fasta"</span></span>
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1143
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1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="python"> <span class="n" style="color: #333;">dirpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)))</span></span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="python"> <span class="n" style="color: #333;">ex_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)),</span><span class="s" style="color: #d14;">'seqsero2_db'</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_09152019: add ex_dir for packaging</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1263" 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">
1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="python"> <span class="n" style="color: #333;">database</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ex_dir</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/H_and_O_and_specific_genes.fasta"</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_09152019: change path to database for packaging</span></span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Note:"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1144" 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="1265" 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">
1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="python"> <span class="n" style="color: #333;">NA_note</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" This predicted serotype is not in the Kauffman-White scheme."</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_09272019: add for new output format</span></span>
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1144
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<td class="diff-line-num new_line" data-linenumber="1266" 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">
1266
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<pre style="margin: 0;"> <span id="LC1266" 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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</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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<td class="diff-line-num old_line" data-linenumber="1145" 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">
1145
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<td class="diff-line-num new_line" data-linenumber="1267" 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">
1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="n" style="color: #333;">dirpath</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/SeqSero2_package.py -h"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#change name of python file</span></span>
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<td class="diff-line-num old_line" data-linenumber="1146" 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">
1146
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<td class="diff-line-num new_line" data-linenumber="1268" 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">
1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1153" 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="1275" 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">@@ -1153,7 +1275,9 @@ def main():</td>
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1153
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<td class="diff-line-num new_line" data-linenumber="1275" 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">
1275
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1154
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<td class="diff-line-num new_line" data-linenumber="1276" 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">
1276
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">([</span><span class="s" style="color: #d14;">"mkdir"</span><span class="p">,</span><span class="n" style="color: #333;">make_dir</span><span class="p">])</span></span>
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1155
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<td class="diff-line-num new_line" data-linenumber="1277" 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">
1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1156" 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">
1156
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<td class="diff-line-num new_line old" data-linenumber="1278" 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="LC1156" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"ln -sr "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dirpath</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;">database</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="o" style="font-weight: 600;">.</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="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;">make_dir</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1157" 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="1278" 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">
1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1157" 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="1279" 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">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"ln -f -s "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">database</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="o" style="font-weight: 600;">.</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="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;">make_dir</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_09152019: change path to database for packaging </span></span>
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<td class="diff-line-num new old_line" data-linenumber="1157" 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="1280" 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">
1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### ed_SL_05282019: use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument).</span></span>
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1157
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<td class="diff-line-num new_line" data-linenumber="1281" 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">
1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">############################begin the real analysis </span></span>
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1158
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<td class="diff-line-num new_line" data-linenumber="1282" 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">
1282
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">analysis_mode</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"a"</span><span class="p">:</span></span>
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1159
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<td class="diff-line-num new_line" data-linenumber="1283" 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">
1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">data_type</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span><span class="s" style="color: #d14;">"2"</span><span class="p">,</span><span class="s" style="color: #d14;">"3"</span><span class="p">]:</span><span class="c1" style="color: #998; font-style: italic;">#use allele mode</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">@@ -1165,7 +1289,7 @@ def main():</td>
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1165
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="python"> <span class="n" style="color: #333;">current_time</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">Y_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">m_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">H_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">M_</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">S"</span><span class="p">,</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">localtime</span><span class="p">())</span></span>
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<td class="diff-line-num old_line" data-linenumber="1166" 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">
1166
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<td class="diff-line-num new_line" data-linenumber="1290" 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">
1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="python"> <span class="n" style="color: #333;">sam</span><span class="p">,</span><span class="n" style="color: #333;">bam</span><span class="p">,</span><span class="n" style="color: #333;">sorted_bam</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq1</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq2</span><span class="p">,</span><span class="n" style="color: #333;">combined_fq</span><span class="p">,</span><span class="n" style="color: #333;">for_sai</span><span class="p">,</span><span class="n" style="color: #333;">rev_sai</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_temp_file_names</span><span class="p">(</span><span class="n" style="color: #333;">fnameA</span><span class="p">,</span><span class="n" style="color: #333;">fnameB</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#get temp files id</span></span>
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<td class="diff-line-num old_line" data-linenumber="1167" 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">
1167
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<td class="diff-line-num new_line" data-linenumber="1291" 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">
1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="python"> <span class="n" style="color: #333;">map_and_sort</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">,</span><span class="n" style="color: #333;">database</span><span class="p">,</span><span class="n" style="color: #333;">fnameA</span><span class="p">,</span><span class="n" style="color: #333;">fnameB</span><span class="p">,</span><span class="n" style="color: #333;">sam</span><span class="p">,</span><span class="n" style="color: #333;">bam</span><span class="p">,</span><span class="n" style="color: #333;">for_sai</span><span class="p">,</span><span class="n" style="color: #333;">rev_sai</span><span class="p">,</span><span class="n" style="color: #333;">sorted_bam</span><span class="p">,</span><span class="n" style="color: #333;">mapping_mode</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#do mapping and sort</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1168" 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">
1168
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1168" class="line" lang="python"> <span class="n" style="color: #333;">xmlfile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extract_mapped_reads_and_do_assembly_and_blast</span><span class="p">(</span><span class="n" style="color: #333;">current_time</span><span class="p">,</span><span class="n" style="color: #333;">sorted_bam</span><span class="p">,</span><span class="n" style="color: #333;">combined_fq</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq1</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq2</span><span class="p">,</span><span class="n" style="color: #333;">threads</span><span class="p">,</span><span class="n" style="color: #333;">fnameA</span><span class="p">,</span><span class="n" style="color: #333;">fnameB</span><span class="p">,</span><span class="n" style="color: #333;">database</span><span class="p">,</span><span class="n" style="color: #333;">mapping_mode</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#extract the mapped reads and do micro assembly and blast</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1169" 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="1292" 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">
1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="python"> <span class="n" style="color: #333;">xmlfile</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff right">new_fasta</span></span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extract_mapped_reads_and_do_assembly_and_blast</span><span class="p">(</span><span class="n" style="color: #333;">current_time</span><span class="p">,</span><span class="n" style="color: #333;">sorted_bam</span><span class="p">,</span><span class="n" style="color: #333;">combined_fq</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq1</span><span class="p">,</span><span class="n" style="color: #333;">mapped_fq2</span><span class="p">,</span><span class="n" style="color: #333;">threads</span><span class="p">,</span><span class="n" style="color: #333;">fnameA</span><span class="p">,</span><span class="n" style="color: #333;">fnameB</span><span class="p">,</span><span class="n" style="color: #333;">database</span><span class="p">,</span><span class="n" style="color: #333;">mapping_mode</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#extract the mapped reads and do micro assembly and blast</span></span>
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<td class="diff-line-num old_line" data-linenumber="1169" 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">
1169
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1293
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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">xmlfile</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"NA"</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="1170" 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">
1170
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<td class="diff-line-num new_line" data-linenumber="1294" 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">
1294
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">fliC_choice</span><span class="p">,</span><span class="n" style="color: #333;">fljB_choice</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="p">,</span><span class="n" style="color: #333;">contamination_H</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="s" style="color: #d14;">"-"</span><span class="p">,</span><span class="s" style="color: #d14;">"-"</span><span class="p">,[],</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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1171
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1295
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1174" 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="1298" 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">@@ -1174,36 +1298,89 @@ def main():</td>
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1174
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<td class="diff-line-num new_line" data-linenumber="1298" 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">
1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Final_list</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="1175" 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">
1175
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<td class="diff-line-num new_line" data-linenumber="1299" 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">
1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">y</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</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 class="p">)</span></span>
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1176
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<td class="diff-line-num new_line" data-linenumber="1300" 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">
1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1177" 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">
1177
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<td class="diff-line-num new_line old" data-linenumber="1301" 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="LC1177" class="line" lang="python"> <span class="n" style="color: #333;">Final_list_passed</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Final_list</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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="mf" style="color: #099;">0.9</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">x</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"__"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"___"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</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="mi" style="color: #099;">1000</span><span class="p">)]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1178" 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">
1178
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<pre style="margin: 0;">-<span id="LC1178" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">fliC_choice</span><span class="p">,</span><span class="n" style="color: #333;">fljB_choice</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="p">,</span><span class="n" style="color: #333;">contamination_H</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="n" style="color: #333;"><span class="idiff">predict_O_and_H_types</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Final_list</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">Final_list_passed</span></span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#predict O, fliC and fljB</span></span>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="python"> <span class="n" style="color: #333;">Final_list_passed</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Final_list</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_cov_"</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 class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"_"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span><span class="o" style="font-weight: 600;">>=</span><span class="mf" style="color: #099;">0.9</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">x</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"__"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"___"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</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="mi" style="color: #099;">1000</span><span class="p">)]</span></span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">fliC_choice</span><span class="p">,</span><span class="n" style="color: #333;">fljB_choice</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">contamination_O</span><span class="p">,</span><span class="n" style="color: #333;">contamination_H</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">Otypes_uniq</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">H1_cont_stat_list</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">H2_cont_stat_list</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">predict_O_and_H_types</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Final_list</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">Final_list_passed</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">new_fasta</span></span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#predict O, fliC and fljB</span></span>
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<td class="diff-line-num old_line" data-linenumber="1179" 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">
1179
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="python"> <span class="n" style="color: #333;">subspecies</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">judge_subspecies</span><span class="p">(</span><span class="n" style="color: #333;">fnameA</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#predict subspecies</span></span>
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1180
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1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">###output</span></span>
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<td class="diff-line-num old_line" data-linenumber="1181" 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">
1181
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1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="python"> <span class="n" style="color: #333;">predict_form</span><span class="p">,</span><span class="n" style="color: #333;">predict_sero</span><span class="p">,</span><span class="n" style="color: #333;">star</span><span class="p">,</span><span class="n" style="color: #333;">star_line</span><span class="p">,</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">seqsero_from_formula_to_serotypes</span><span class="p">(</span><span class="n" style="color: #333;">O_choice</span><span class="p">,</span><span class="n" style="color: #333;">fliC_choice</span><span class="p">,</span><span class="n" style="color: #333;">fljB_choice</span><span class="p">,</span><span class="n" style="color: #333;">special_gene_list</span><span class="p">,</span><span class="n" style="color: #333;">subspecies</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1182" 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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1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="python"> <span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span> <span class="c1" style="color: #998; font-style: italic;">#04132019, disable claim for new report requirement</span></span>
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1182
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="python"> <span class="n" style="color: #333;">H_list</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"fliC_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">H1_cont_stat_list</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</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 class="o" style="font-weight: 600;">+</span><span class="p">[</span><span class="s" style="color: #d14;">"fljB_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">H2_cont_stat_list</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</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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1183
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1309
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<pre style="margin: 0;"> <span id="LC1309" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contamination_O</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">contamination_H</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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1184
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<td class="diff-line-num new_line old" data-linenumber="1310" 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="LC1184" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#<span class="idiff left">detected potential contamination of mixed serotypes from O antigen signals.</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1185" 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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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#<span class="idiff left">Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Otypes_uniq</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">".</span>"</span></span>
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1185
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<td class="diff-line-num new_line" data-linenumber="1311" 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">
1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">contamination_O</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">contamination_H</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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1186
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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#<span class="idiff left">detected potential contamination of mixed serotypes or potential thrid H phase from H antigen signals.</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span></span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1187" 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="1312" 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">
1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#<span class="idiff left">Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">H_list</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">".</span>"</span></span>
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1187
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<td class="diff-line-num new_line" data-linenumber="1313" 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">
1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">contamination_O</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">contamination_H</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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1188
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<td class="diff-line-num new_line old" data-linenumber="1314" 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="LC1188" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#detected potential contamination of mixed serotypes from both O and H antigen signals.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1189" 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="1314" 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">
1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">Otypes_uniq</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">". All H-antigens detected:"</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">H_list</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1315" 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">
1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">!=</span><span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1189" 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="1316" 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">
1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1317" 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">
1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="python"> <span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1318" 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">
1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1319" 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">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">## ed_SL_09272019: change for new output format</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1320" 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">
1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if contamination_report+star_line+claim=="": #0413, new output style</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1321" 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">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># note=""</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1322" 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">
1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#else:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1323" 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">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># note="Note:"</span></span>
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1189
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<td class="diff-line-num new_line" data-linenumber="1324" 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">
1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clean_mode</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="1190" 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">
1190
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<td class="diff-line-num new_line" data-linenumber="1325" 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">
1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"rm -rf ../"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1191
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<td class="diff-line-num new_line" data-linenumber="1326" 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">
1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="python"> <span class="n" style="color: #333;">make_dir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"none-output-directory due to '-c' flag"</span></span>
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1192
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<td class="diff-line-num new_line" data-linenumber="1327" 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">
1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1193
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<td class="diff-line-num new_line old" data-linenumber="1328" 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="LC1193" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"Seq<span class="idiff left right">s</span>ero_result.txt"</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"Seq<span class="idiff left right">S</span>ero_result.txt"</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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1194
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1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">O_choice</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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1195
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1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"-"</span></span>
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1196
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<pre style="margin: 0;">-<span id="LC1196" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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;">Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">for_fq</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;">rev_fq</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 class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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 class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fliC_choice</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 class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fljB_choice</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 class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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 class="s" style="color: #d14;">"Predicted serotype(s):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star</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 class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"N/A"</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;">predict_sero</span><span class="p">:</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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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<td class="diff-line-num new new_line" data-linenumber="1333" 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">
1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</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;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">input_file</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 class="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1334" 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">
1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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<td class="diff-line-num new new_line" data-linenumber="1335" 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">
1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fliC_choice</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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<td class="diff-line-num new new_line" data-linenumber="1336" 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">
1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fljB_choice</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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<td class="diff-line-num new new_line" data-linenumber="1337" 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">
1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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<td class="diff-line-num new new_line" data-linenumber="1338" 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">
1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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<td class="diff-line-num new new_line" data-linenumber="1339" 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">
1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: change serotype(s) to serotype</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1341" 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">
1341
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<pre style="margin: 0;">+<span id="LC1341" 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="LC1342" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"</span></span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span> <span class="c1" style="color: #998; font-style: italic;">#04132019, for new output requirement, diable star_line if "NA" in output</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</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;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">input_file</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 class="o" style="font-weight: 600;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1346" 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">
1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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<td class="diff-line-num new new_line" data-linenumber="1347" 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">
1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fliC_choice</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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<td class="diff-line-num new new_line" data-linenumber="1348" 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">
1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fljB_choice</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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<td class="diff-line-num new new_line" data-linenumber="1349" 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">
1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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<td class="diff-line-num new new_line" data-linenumber="1351" 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">
1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_09242019: add serotype output for "N/A" prediction</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">NA_note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1197
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1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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1198
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1354
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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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1199
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1355
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#subprocess.check_call("cat Seqsero_result.txt",shell=True)</span></span>
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1200
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True)</span></span>
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1201
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1357
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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">"rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fnameA</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"*_db* 2> /dev/null"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1202
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<pre style="margin: 0;">-<span id="LC1202" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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;">Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">for_fq</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;">rev_fq</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 class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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 class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fliC_choice</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 class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fljB_choice</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 class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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 class="s" style="color: #d14;">"Predicted serotype(s):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star</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 class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1358" 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">
1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"N/A"</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;">predict_sero</span><span class="p">:</span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+##</span></span>
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1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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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1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</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;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">input_file</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 class="o" style="font-weight: 600;">+</span></span>
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1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fliC_choice</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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<td class="diff-line-num new new_line" data-linenumber="1364" 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">
1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fljB_choice</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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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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<td class="diff-line-num new new_line" data-linenumber="1367" 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">
1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: change serotype(s) to serotype</span></span>
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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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="LC1371" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</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;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">input_file</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 class="o" style="font-weight: 600;">+</span></span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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<td class="diff-line-num new new_line" data-linenumber="1373" 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">
1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fliC_choice</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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<td class="diff-line-num new new_line" data-linenumber="1374" 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">
1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fljB_choice</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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<td class="diff-line-num new new_line" data-linenumber="1375" 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">
1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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<td class="diff-line-num new new_line" data-linenumber="1376" 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">
1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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<td class="diff-line-num new new_line" data-linenumber="1377" 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">
1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_09242019: add serotype output for "N/A" prediction</span></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">NA_note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">contamination_report</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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1203
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1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1204
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1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'"</span><span class="p">)</span></span>
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1205
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1381
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">analysis_mode</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"k"</span><span class="p">:</span></span>
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1206
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<td class="diff-line-num new_line old" data-linenumber="1382" 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="LC1206" class="line" lang="python"> <span class="n" style="color: #333;">ex_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">))</span></span>
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1382
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#ex_dir = os.path.dirname(os.path.realpath(__file__))</span></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="python"> <span class="n" style="color: #333;">ex_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)),</span><span class="s" style="color: #d14;">'seqsero2_db'</span><span class="p">))</span> <span class="c1" style="color: #998; font-style: italic;"># ed_SL_09152019: change ex_dir for packaging</span></span>
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1207
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1384
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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#output_mode = args.mode</span></span>
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1208
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1385
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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="python"> <span class="n" style="color: #333;">for_fq</span><span class="p">,</span><span class="n" style="color: #333;">rev_fq</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_input_files</span><span class="p">(</span><span class="n" style="color: #333;">make_dir</span><span class="p">,</span><span class="n" style="color: #333;">input_file</span><span class="p">,</span><span class="n" style="color: #333;">data_type</span><span class="p">,</span><span class="n" style="color: #333;">dirpath</span><span class="p">)</span></span>
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1209
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1386
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<pre style="margin: 0;"> <span id="LC1386" 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;">for_fq</span> <span class="c1" style="color: #998; font-style: italic;">#-k will just use forward because not all reads were used</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">@@ -1219,20 +1396,73 @@ def main():</td>
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1219
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1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="python"> <span class="n" style="color: #333;">subspecies</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"II"</span></span>
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1220
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1397
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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="python"> <span class="n" style="color: #333;">predict_form</span><span class="p">,</span><span class="n" style="color: #333;">predict_sero</span><span class="p">,</span><span class="n" style="color: #333;">star</span><span class="p">,</span><span class="n" style="color: #333;">star_line</span><span class="p">,</span><span class="n" style="color: #333;">claim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqsero_from_formula_to_serotypes</span><span class="p">(</span></span>
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1221
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1398
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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="python"> <span class="n" style="color: #333;">highest_O</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">highest_fliC</span><span class="p">,</span> <span class="n" style="color: #333;">highest_fljB</span><span class="p">,</span> <span class="n" style="color: #333;">Special_dict</span><span class="p">,</span><span class="n" style="color: #333;">subspecies</span><span class="p">)</span></span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" class="line" lang="python"> <span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span> <span class="c1" style="color: #998; font-style: italic;">#no claim any more based on new output requirement</span></span>
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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">## ed_SL_09272019: change for new output format</span></span>
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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if star_line+claim=="": #0413, new output style</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># note=""</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#else:</span></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># note="Note:"</span></span>
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1222
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1405
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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clean_mode</span><span class="p">:</span></span>
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1223
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1406
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">"rm -rf ../"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1224
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="python"> <span class="n" style="color: #333;">make_dir</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"none-output-directory due to '-c' flag"</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c"</span></span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">highest_O</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</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="LC1411" 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="LC1412" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">highest_O</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">###</span></span>
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1225
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1226
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">highest_O</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">""</span><span class="p">:</span></span>
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1227
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1416
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"-"</span></span>
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1228
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1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1229
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1418
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="python"> <span class="n" style="color: #333;">O_choice</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">highest_O</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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1230
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<td class="diff-line-num new_line" data-linenumber="1419" 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">
1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero)</span></span>
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1231
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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"Seqsero_result.txt"</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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1232
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<td class="diff-line-num new_line old" data-linenumber="1420" 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="LC1232" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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;">Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input_file</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 class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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 class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fliC</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 class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fljB</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 class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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 class="s" style="color: #d14;">"Predicted serotype(s):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star</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 class="n" style="color: #333;">star</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"SeqSero_result.txt"</span><span class="p">,</span><span class="s" style="color: #d14;">"w"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1421" 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">
1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##</span></span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"N/A"</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;">predict_sero</span><span class="p">:</span></span>
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1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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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<td class="diff-line-num new new_line" data-linenumber="1424" 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">
1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input_file</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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<td class="diff-line-num new new_line" data-linenumber="1425" 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">
1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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<td class="diff-line-num new new_line" data-linenumber="1426" 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">
1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fliC</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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<td class="diff-line-num new new_line" data-linenumber="1427" 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">
1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fljB</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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<td class="diff-line-num new new_line" data-linenumber="1428" 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">
1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: change serotype(s) to serotype</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1431" 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">
1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1432" 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">
1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1434" 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">
1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="python"> <span class="n" style="color: #333;">star_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span> <span class="c1" style="color: #998; font-style: italic;">#changed for new output requirement, 04132019</span></span>
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1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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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<td class="diff-line-num new new_line" data-linenumber="1436" 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">
1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input_file</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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1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fliC</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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1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fljB</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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1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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<td class="diff-line-num new new_line" data-linenumber="1442" 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">
1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_09242019: add serotype output for "N/A" prediction</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1443" 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">
1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">NA_note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1233
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="python"> <span class="n" style="color: #333;">new_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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1234
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1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="s" style="color: #d14;">"rm *.fasta* *.fastq *.gz *.fq temp.txt *.sra 2> /dev/null"</span><span class="p">,</span><span class="n" style="color: #333;">shell</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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1235
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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;">Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input_file</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 class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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 class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fliC</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 class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fljB</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 class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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 class="s" style="color: #d14;">"Predicted serotype(s):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star</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 class="n" style="color: #333;">star</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"N/A"</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;">predict_sero</span><span class="p">:</span></span>
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1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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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1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input_file</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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1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fliC</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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1451
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fljB</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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1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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1453
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<pre style="margin: 0;">+<span id="LC1453" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_sero</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_04152019: change serotype(s) to serotype</span></span>
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1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Output_directory:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">make_dir</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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1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="python"> <span class="s" style="color: #d14;">"Input files:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input_file</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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1459
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<pre style="margin: 0;">+<span id="LC1459" class="line" lang="python"> <span class="s" style="color: #d14;">"O antigen prediction:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">O_choice</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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1460
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<pre style="margin: 0;">+<span id="LC1460" class="line" lang="python"> <span class="s" style="color: #d14;">"H1 antigen prediction(fliC):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fliC</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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1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="python"> <span class="s" style="color: #d14;">"H2 antigen prediction(fljB):</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">highest_fljB</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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1462
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<pre style="margin: 0;">+<span id="LC1462" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted subspecies:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">subspecies</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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1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted antigenic profile:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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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<td class="diff-line-num new new_line" data-linenumber="1464" 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">
1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="python"> <span class="s" style="color: #d14;">"Predicted serotype:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">predict_form</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 class="c1" style="color: #998; font-style: italic;"># ed_SL_09242019: add serotype output for "N/A" prediction</span></span>
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="python"> <span class="n" style="color: #333;">note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">NA_note</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">star_line</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">claim</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">#+##</span></span>
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1236
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1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="python"></span>
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1237
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1467
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<pre style="margin: 0;"> <span id="LC1467" 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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1468
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<pre style="margin: 0;"> <span id="LC1468" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">seqsero2 (<span class="idiff left right">0.1</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seqsero2 (<span class="idiff left right">1.0.2</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #??)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 31 Jan 2019 08:16:55</span> +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 11 Dec 2019 16:19:03</span> +0100</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</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">@@ -3,24 +3,28 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python<span class="idiff left right">3</span>,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> bwa,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> sra-toolkit</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">4</span>.1</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/seqsero2</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/seqsero2.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/denglab/SeqSero2</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: seqsero2</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Depends: ${python:Depends},</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Depends: ${python<span class="idiff left right">3</span>:Depends},</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> python-biopython,</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> bwa,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> sra-toolkit</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ncbi-blast+,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> sra-toolkit,</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> spades,</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> bedtools,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> salmid</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Description: Salmonella serotyping from genome sequencing data</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> SeqSero2 is a pipeline for Salmonella serotype determination from raw</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> sequencing reads or genome assemblies.</span>
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<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> dh $@ --with python<span class="idiff left right">3 --buildsystem=pybuild</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">override_dh_fixperms:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh_fixperms</span>
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<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: ></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Shaokang Zhang and Yanlong Yin and Marcus B. Jones and Zhenzhen Zhang and</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Brooke L. Deatherage Kaiser and Blake A. Dinsmore and Collette Fitzgerald</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> and Patricia I. Fields and Xiangyu Deng</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Title: ></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Salmonella Serotype Determination Utilizing High-throughput</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Genome Sequencing Data</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Journal: Journal of Clinical Microbiology</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Year: 2015</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Volume: 53</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> Number: 5</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> Pages: 1685-92</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> DOI: 10.1128/JCM.00323-15</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> PMID: 25762776</span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> URL: "http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15"</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> eprint: ></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15.full.pdf+html</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> <span class="idiff left right"> </span>Author: ></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right"> </span>Shaokang Zhang and Yanlong Yin and Marcus B. Jones and Zhenzhen Zhang and</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>Brooke L. Deatherage Kaiser and Blake A. Dinsmore and Collette Fitzgerald</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>and Patricia I. Fields and Xiangyu Deng</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: ></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Salmonella Serotype Determination Utilizing High-throughput</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Genome Sequencing Data</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Journal of Clinical Microbiology</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2015</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 53</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 5</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: 1685-92</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1128/JCM.00323-15</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 25762776</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: "http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15"</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> <span class="idiff left right"> </span>eprint: ></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> <span class="idiff left right"> </span>http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15.full.pdf+html</span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Registry:</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> - Name: OMICtools</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> Entry: OMICS_21700</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> - Name: bio.tools</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> Entry: NA</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> Entry: seqsero2</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> - Name: SciCrunch</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> Entry: NA</span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: OMICtools</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: OMICS_21700</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- Name: bio.tools</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Entry: NA</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Entry: seqsero2</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">- Name: SciCrunch</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Entry: NA</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Bug-Database: https://github.com/denglab/SeqSero2/issues</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Repository: https://github.com/denglab/SeqSero2.git</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Repository-Browse: https://github.com/denglab/SeqSero2</span></pre>
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<li id="8027f83a71b6358278b6bf0be04a8b7188dfc64b">
<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#8027f83a71b6358278b6bf0be04a8b7188dfc64b"><strong>seqsero2_db/H_and_O_and_specific_genes.fasta</strong></a>
The diff for this file was not included because it is too large.
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<li id="787186626ffc5d4caa57767f0bc18bf1cc6641f4">
<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#787186626ffc5d4caa57767f0bc18bf1cc6641f4"><strong>antigens.pickle</strong>
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<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#bc4f385db6d82f0fcb514281606f054f16305217"><strong>invA_mers_dict</strong>
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<strong>seqsero2_db/invA_mers_dict</strong>
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<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#468dd2b4378046cc4d14ea51ad36846f59ab327e"><strong>special.pickle</strong>
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<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">find_packages</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readme</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC6" 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="s" style="color: #d14;">'README.md'</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="LC7" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">setup</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;">'SeqSero2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"version.py"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readlines</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">'"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Salmonella serotyping'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readme</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">'Development Status :: 3 - Alpha'</span><span class="p">,</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">'License :: OSI Approved :: GNU General Public License v2 (GPLv2)'</span><span class="p">,</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3'</span><span class="p">,</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">'Topic :: Text Processing :: Linguistic'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="p">],</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Salmonella serotyping bioinformatics WGS'</span><span class="p">,</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/denglab/SeqSero2/'</span><span class="p">,</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng'</span><span class="p">,</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'GPLv2'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"bin/deinterleave_fastq.sh"</span><span class="p">,</span><span class="s" style="color: #d14;">"bin/Initial_Conditions.py"</span><span class="p">,</span><span class="s" style="color: #d14;">"bin/SeqSero2_package.py"</span><span class="p">,</span><span class="s" style="color: #d14;">"bin/SeqSero2_update_kmer_database.py"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">packages</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>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">include_package_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'biopython==1.73'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">data_files</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">"seqsero2_db"</span><span class="p">,[</span><span class="s" style="color: #d14;">"seqsero2_db/antigens.pickle"</span><span class="p">,</span><span class="s" style="color: #d14;">"seqsero2_db/H_and_O_and_specific_genes.fasta"</span><span class="p">,</span><span class="s" style="color: #d14;">"seqsero2_db/invA_mers_dict"</span><span class="p">,</span><span class="s" style="color: #d14;">"seqsero2_db/special.pickle"</span><span class="p">])],</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">zip_safe</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="LC30" class="line" lang="python"><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/seqsero2/compare/9e20df654d455480f76288dc70afb2dde1fba3f3...bea8e71b7fc2a8613b03d15e757bd584fedcc068#6defec8c57d89c1d5b6d02a6f7adc9f898c9b505"><strong>version.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">SeqSero2_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.0.2'</span></span></pre>
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