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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/busco">Debian Med / busco</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/796d64b186a8ef1c25ffe9d60614420eab3bd6bc">796d64b1</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-07-27T16:47:05+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.1.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/efa8c80f8799169c93f3fe5b2e7d07e463c11a96">efa8c80f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-07-27T16:47:05+02:00</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/busco/-/commit/83624ec5efaf1f80cc42a51f86bcbad6f4999444">83624ec5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-07-27T16:47:08+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/4.1.2'
Update to upstream version '4.1.2'
with Debian dir 0e4645142a4444220eb2b00d9371fcc9c19d8b37</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/c97cf68b05bab379b6ae92899d7408d186873f46">c97cf68b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-07-27T16:47:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/e8352179396aa15684dc0efd9af39d4ec32ff694">e8352179</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-07-27T16:47:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Repository, Repository-Browse.
Changes-By: lintian-brush
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/1c4781f6b08bd870d527196d9dae09387c727d0b">1c4781f6</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-07-27T16:47:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>25 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#2e553dba9eac3b861936b9c662ee7d87c706dea0">
bin/busco
</a>
</li>
<li class="file-stats">
<a href="#80680bd277bcadaacce5cbc6697d87d491a734b6">
config/config.ini
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#2e93f7e0e2fd4edc2763be000d7339cf2a01055c">
src/busco/Analysis.py
</a>
</li>
<li class="file-stats">
<a href="#de7754708bf8aa012a49a842a0d52b6628af3d59">
src/busco/AutoLineage.py
</a>
</li>
<li class="file-stats">
<a href="#bf9cbed51faec015f7b0c0f8d5ec757bb662a62f">
src/busco/BuscoAnalysis.py
</a>
</li>
<li class="file-stats">
<a href="#e497bbf996017c0692c161d2cfed28374276cc73">
src/busco/BuscoConfig.py
</a>
</li>
<li class="file-stats">
<a href="#187e8b3b00a66c92055c44aac0cd5c916c6c913e">
src/busco/BuscoDownloadManager.py
</a>
</li>
<li class="file-stats">
<a href="#ea2771659c3ac27a7eedddf367d04f0deb13246b">
src/busco/BuscoLogger.py
</a>
</li>
<li class="file-stats">
<a href="#414e3994e90f7a52298faa998003b76c548435da">
src/busco/BuscoPlacer.py
</a>
</li>
<li class="file-stats">
<a href="#a8fd6f8fc327bd92758f2c1e85bd45f1bad18df0">
src/busco/BuscoRunner.py
</a>
</li>
<li class="file-stats">
<a href="#200a2d1cfa2fb65158ca0f851c48c1054f174e7a">
src/busco/BuscoTools.py
</a>
</li>
<li class="file-stats">
<a href="#d6ebf611cefbf0b1e0d40019e29253fbd1e6e981">
src/busco/GeneSetAnalysis.py
</a>
</li>
<li class="file-stats">
<a href="#d1bb5c571aba1a9dd63ad9538318c32ffd274023">
src/busco/GenomeAnalysis.py
</a>
</li>
<li class="file-stats">
<a href="#a6fed85d58ca22cbfd88df357244e6f9fc6faa70">
src/busco/Toolset.py
</a>
</li>
<li class="file-stats">
<a href="#a2bbc032e6ed94eee5944cfbd98d5754a5fed726">
src/busco/TranscriptomeAnalysis.py
</a>
</li>
<li class="file-stats">
<a href="#b183fcee25a51af18c90f143ded1ffead1019f47">
<span class="deleted-file">
−
src/busco/ViralAnalysis.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88">
src/busco/_version.py
</a>
</li>
<li class="file-stats">
<a href="#bd0e703ba072ee7447fcc5bd1e634475b3438cf9">
src/busco/run_BUSCO.py
</a>
</li>
<li class="file-stats">
<a href="#dba59ea4008347497ea58386e70f0fd75cc9a2e4">
test_data/bacteria/expected_log.txt
</a>
</li>
<li class="file-stats">
<a href="#11a346fb4c4f7cb01e1e5466e6712687c54fe746">
test_data/eukaryota/expected_log.txt
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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">
1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">4.1.2</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1" 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="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Issue #295 fixed</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">4.1.1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Issue #287 fixed</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">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">4.1.0</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">- Reintroduce restart mode (Issues #203, #229, #251)</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">- Fix augustus hanging problem (Issues #224, #232, #266)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">- Allow multiple cores for BLAST 2.10.1+</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- Issue #271 fixed</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">- Issue #247 fixed</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">- Issue #234 fixed</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">4.0.6</span>
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<td class="diff-line-num old_line" data-linenumber="2" 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">
2
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">- Fix Augustus GFF parsing bug. Remove constraint on Augustus version.</span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**BUSCOv4 - Benchmarking sets of Universal Single-Copy Orthologs.**</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">For full documentation please consult the user guide: https://busco.ezlab.org/busco_userguide.html</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">Main changes in v4:</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">-</span> Automated selection of lineages issued from https://www.orthodb.org/ release 10</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">@@ -14,30 +16,22 @@ To install, clone the repository and enter ``sudo python3 setup.py install`` or</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown">More details in the user guide: https://busco.ezlab.org/busco_userguide.html#manual-installation</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">Do not forget to edit the <span class="sb" style="color: #d14;">``config/config.ini``</span> file to match your environment. The script <span class="sb" style="color: #d14;">`scripts/busco_configurator.py`</span> can help <span class="idiff left">you filling it. You also have to set the </span><span class="sb" style="color: #d14;"><span class="idiff right">``BUSCO_CONFIG_FILE``</span></span> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="idiff left">environment variable to define the path (including the filename) to that </span><span class="sb" style="color: #d14;"><span class="idiff">``config.ini``</span></span><span class="idiff right"> file. It can be located anywhere.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown">Do not forget to edit the <span class="sb" style="color: #d14;">``config/config.ini``</span> file to match your environment. The script <span class="sb" style="color: #d14;">`scripts/busco_configurator.py`</span> can help <span class="idiff left right">with this.</span> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="idiff left">You can set the </span><span class="sb" style="color: #d14;"><span class="idiff">``BUSCO_CONFIG_FILE``</span></span><span class="idiff"> environment variable to define the path (including the filename) to that </span><span class="sb" style="color: #d14;"><span class="idiff">``config.ini``</span></span><span class="idiff right"> file. </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="LC22" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown">export BUSCO_CONFIG_FILE="/path/to/myconfig.ini"</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">Alternatively you can pass the config file path as a command line argument using <span class="sb" style="color: #d14;">``--config /path/to/config.ini``</span>.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></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="LC28" class="line" lang="markdown">If you have trouble installing one of the many third-party tools, try the official Docker container: https://hub.docker.com/r/ezlabgva/busco/tags</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="LC30" class="line" lang="markdown">Report problems on the BUSCO issue board at https://gitlab.com/ezlab/busco/issues</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="LC28" class="line" lang="markdown">To get help on BUSCO use: <span class="sb" style="color: #d14;">``busco -h``</span> and <span class="sb" style="color: #d14;">``python3 scripts/generate_plot.py -h``</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="LC30" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**!!!**</span> Don't use "odb9" datasets with BUSCOv4. If you need to reproduce previous analyses, use BUSCOv3 (https://gitlab.com/ezlab/busco/-/tags/3.0.2)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">To get help with BUSCO use: <span class="sb" style="color: #d14;">``busco -h``</span> and <span class="sb" style="color: #d14;">``python3 scripts/generate_plot.py -h``</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">Note: For v4.0.2 and before, when running auto-lineage, the initial results for eukaryotes were incomplete. This was </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">deliberate, as these initial results are used merely to determine whether the genome scores highest against the </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown">bacteria, archaea or eukaryota datasets. If the eukaryota dataset was selected, BUSCO then attempts to place the input </span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown">assembly on the eukaryote phylogenetic tree before running a complete BUSCO assessment using the selected child dataset. </span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown">Unless the top-level eukaryota dataset was selected as the best match for the input file, the eukaryota dataset run </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown">would not complete. So while the specific dataset run returned accurate results, the generic eukaryota dataset run </span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown">should be considered unreliable. </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown">This has been changed in v4.0.3. The eukaryota run now always completes so the final generic eukaryota results can be </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown">considered reliable.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**!!!**</span> Do not use "odb9" datasets with BUSCOv4. If you need to reproduce previous analyses, use BUSCOv3 (https://gitlab.com/ezlab/busco/-/tags/3.0.2)</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**How to cite BUSCO**</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#2e553dba9eac3b861936b9c662ee7d87c706dea0"><strong>bin/busco</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">@@ -8,14 +8,16 @@ except ImportError as err:</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">pattern_search</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"cannot import name '(?P<module_name>[\w]+)"</span><span class="p">,</span> <span class="n" style="color: #333;">err</span><span class="p">.</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">missing_module</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern_search</span><span class="p">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="s" style="color: #d14;">"module_name"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing_module</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"run_BUSCO"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"BUSCO must be installed before it is run. Please enter 'python setup.py install (--user)'. See the user guide for more information."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"BUSCO must be installed before it is run. Please enter 'python setup.py install (--user)'. "</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">"See the user guide for more information."</span><span class="p">)</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">missing_module</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Bio"</span><span class="p">:</span></span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Please install BioPython (https://biopython.org/) before running BUSCO."</span><span class="p">)</span></span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">missing_module</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"numpy"</span><span class="p">:</span></span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Please install NumPy before running BUSCO."</span><span class="p">)</span></span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to find module {}. Please make sure it is installed. See the user guide and the GitLab issue "</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"board (https://gitlab.com/ezlab/busco/issues) if you need further assistance."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">missing_module</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"board (https://gitlab.com/ezlab/busco/issues) if you need further assistance."</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">missing_module</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>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="p">.</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" 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="25" 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">@@ -23,4 +25,4 @@ except ImportError as err:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">"GitLab issue board (https://gitlab.com/ezlab/busco/issues) if you need further assistance."</span><span class="p">)</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="n" style="color: #333;">run_BUSCO</span><span class="p">.</span><span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">run_BUSCO</span><span class="p">.</span><span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<li id="80680bd277bcadaacce5cbc6697d87d491a734b6">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#80680bd277bcadaacce5cbc6697d87d491a734b6"><strong>config/config.ini</strong></a>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># Many of the options in the busco_run section can alternatively be set using command line arguments. See the help prompt (busco -h) for details.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># WARNING: passing a parameter through the command line overrides the value specified in this file.</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># You need to set the path to this file in the environment variable BUSCO_CONFIG_<span class="idiff left right">PATH</span></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># You need to set the path to this file in the environment variable BUSCO_CONFIG_<span class="idiff left right">FILE</span></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># as follows:</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># export BUSCO_CONFIG_FILE="/path/to/myconfig.ini"</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;">;cpu = 16</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># Force rewrite if files already exist (True/False)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;">;force = False</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># Restart a previous BUSCO run (True/False)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;">;restart = False</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># Blast e-value</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;">;evalue = 1e-3</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;"># How many candidate regions (contigs, scaffolds) to consider for each BUSCO</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">@@ -56,11 +58,11 @@</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="ini"><span class="c" style="color: #998; font-style: italic;">;update-data = True</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="ini"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="ini"><span class="nn" style="color: #555;">[tblastn]</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="ini"><span class="py">path</span> <span class="p">=</span> <span class="s" style="color: #d14;">/ncbi-blast-2.<span class="idiff left right">2.3</span>1+/bin/</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="ini"><span class="py">path</span> <span class="p">=</span> <span class="s" style="color: #d14;">/ncbi-blast-2.<span class="idiff left right">10.</span>1+/bin/</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="ini"><span class="py">command</span> <span class="p">=</span> <span class="s" style="color: #d14;">tblastn</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="ini"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="ini"><span class="nn" style="color: #555;">[makeblastdb]</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="ini"><span class="py">path</span> <span class="p">=</span> <span class="s" style="color: #d14;">/ncbi-blast-2.<span class="idiff left right">2.3</span>1+/bin/</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="ini"><span class="py">path</span> <span class="p">=</span> <span class="s" style="color: #d14;">/ncbi-blast-2.<span class="idiff left right">10.</span>1+/bin/</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="ini"><span class="py">command</span> <span class="p">=</span> <span class="s" style="color: #d14;">makeblastdb</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="ini"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="ini"><span class="nn" style="color: #555;">[augustus]</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">busco (4.1.2-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Set upstream metadata fields: Repository, Repository-Browse.</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"> -- Steffen Moeller <moeller@debian.org> Mon, 27 Jul 2020 16:47:16 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">busco (4.0.6-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</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"> python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools</span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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">@@ -15,3 +15,5 @@ Reference:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> Entry: busco</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Repository: https://gitlab.com/ezlab/busco.git</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Repository-Browse: https://gitlab.com/ezlab/busco</span></pre>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#2e93f7e0e2fd4edc2763be000d7339cf2a01055c"><strong>src/busco/Analysis.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" 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="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoTools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TBLASTNRunner</span><span class="p">,</span> <span class="n" style="color: #333;">MKBLASTRunner</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;">busco.Toolset</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Tool</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;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoLogger</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">LogDecorator</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">log</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABCMeta</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">abstractmethod</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABCMeta</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,26 +14,13 @@ class NucleotideAnalysis(metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># explanation of ambiguous codes found here: https://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">AMBIGUOUS_CODES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"R"</span><span class="p">,</span> <span class="s" style="color: #d14;">"W"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S"</span><span class="p">,</span> <span class="s" style="color: #d14;">"K"</span><span class="p">,</span> <span class="s" style="color: #d14;">"M"</span><span class="p">,</span> <span class="s" style="color: #d14;">"D"</span><span class="p">,</span> <span class="s" style="color: #d14;">"V"</span><span class="p">,</span> <span class="s" style="color: #d14;">"H"</span><span class="p">,</span> <span class="s" style="color: #d14;">"B"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">MAX_FLANK</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20000</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Variables inherited from BuscoAnalysis</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Initialize BuscoAnalysis</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"long"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_flank</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_define_flank</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ev_cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">getfloat</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"evalue"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_region_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">getint</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"limit"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blast_cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># Initialize BuscoAnalysis</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_nucleotide_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Please provide a nucleotide file as input"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_nucleotide_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">i</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="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">letter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">upper</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">@@ -51,66 +35,43 @@ class NucleotideAnalysis(metaclass=ABCMeta):</td>
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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="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_define_flank</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> TODO: Add docstring</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC59" 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="LC60" class="line" lang="python"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">getsize</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="mi" style="color: #099;">1000</span> <span class="c1" style="color: #998; font-style: italic;"># size in mb</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">flank</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;">size</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">50</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># proportional flank size</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Ensure value is between 5000 and MAX_FLANK</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">flank</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">flank</span><span class="p">,</span> <span class="mi" style="color: #099;">5000</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">MAX_FLANK</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Input data is only validated during run_analysis. This will catch any IO issues before that.</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Impossible to read the fasta file {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">flank</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: This should be an abstract method</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> Initialize all required tools for Genome Eukaryote Analysis:</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> MKBlast, TBlastn, Augustus and Augustus scripts: GFF2GBSmallDNA, new_species, etraining</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">init_tools</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MKBLASTRunner</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TBLASTNRunner</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_tool_dependencies</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">check_tool_dependencies</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_blast_version</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">mkblastdb_version_call</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mkblast_tool</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="s" style="color: #d14;">"-version"</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;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">mkblastdb_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">mkblastdb_version_call</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">rsplit</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="LC85" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">tblastn_version_call</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="s" style="color: #d14;">"-version"</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;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">tblastn_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tblastn_version_call</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">rsplit</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="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mkblastdb_version</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">tblastn_version</span><span class="p">:</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"You are using version {} of mkblastdb and version {} of tblastn."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">mkblastdb_version</span><span class="p">,</span> <span class="n" style="color: #333;">tblastn_version</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tblastn_version</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">:</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"You are using version {} of makeblastdb and version {} of tblastn."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">))</span></span>
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93
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_mkblast</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MKBLASTRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mkblast_tool</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping makeblastdb as BLAST DB already exists at {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_db</span><span class="p">))</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="c1" style="color: #998; font-style: italic;"># Turn off restart mode if this is the entry point</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC54" 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;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_db</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"makeblastdb failed to create a BLAST DB at {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_db</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_tblastn</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">missing_and_frag_only</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">ancestral_variants</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">incomplete_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">missing_buscos</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">fragmented_buscos</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing_and_frag_only</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># This parameter is only used on the re-run</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TBLASTNRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_db</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ev_cutoff</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blast_cpus</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_region_limit</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_flank</span><span class="p">,</span> <span class="n" style="color: #333;">missing_and_frag_only</span><span class="p">,</span> <span class="n" style="color: #333;">ancestral_variants</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">incomplete_buscos</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">_get_coordinates</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">_filter_best_matches</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Todo: remove underscores from non-hidden methods</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">_write_coordinates_to_file</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># writes to "coordinates.tsv"</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">_write_contigs</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">coords</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">configure_runner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_db</span><span class="p">,</span> <span class="n" style="color: #333;">missing_and_frag_only</span><span class="p">,</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">ancestral_variants</span><span class="p">,</span> <span class="n" style="color: #333;">incomplete_buscos</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping tblastn as results already exist at {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">blast_filename</span><span class="p">))</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">get_coordinates</span><span class="p">()</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">filter_best_matches</span><span class="p">()</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">write_coordinates_to_file</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># writes to "coordinates.tsv"</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">write_contigs</span><span class="p">()</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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114
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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115
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>
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116
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ProteinAnalysis</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" 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="79" 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">@@ -118,8 +79,8 @@ class ProteinAnalysis:</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">LETTERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"F"</span><span class="p">,</span> <span class="s" style="color: #d14;">"L"</span><span class="p">,</span> <span class="s" style="color: #d14;">"I"</span><span class="p">,</span> <span class="s" style="color: #d14;">"M"</span><span class="p">,</span> <span class="s" style="color: #d14;">"V"</span><span class="p">,</span> <span class="s" style="color: #d14;">"S"</span><span class="p">,</span> <span class="s" style="color: #d14;">"P"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"X"</span><span class="p">,</span> <span class="s" style="color: #d14;">"H"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"N"</span><span class="p">,</span> <span class="s" style="color: #d14;">"K"</span><span class="p">,</span> <span class="s" style="color: #d14;">"D"</span><span class="p">,</span> <span class="s" style="color: #d14;">"E"</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"W"</span><span class="p">,</span> <span class="s" style="color: #d14;">"R"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">NUCL_LETTERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="s" style="color: #d14;">"N"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">config</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">config</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_protein_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">):</span></span>
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124
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">'Please provide a protein file as input'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"></span>
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<li id="de7754708bf8aa012a49a842a0d52b6628af3d59">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#de7754708bf8aa012a49a842a0d52b6628af3d59"><strong>src/busco/AutoLineage.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,7 +71,7 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">root_runners</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_lineages_list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">all_lineages</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_best_match_lineage</span><span class="p">(</span><span class="n" style="color: #333;">root_runners</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain_run_name"</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">best_match_lineage_dataset</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_r<span class="idiff left">unner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">hmmer_r</span>esults_lines</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">results_datasets</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">best_match_lineage_dataset</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC77" 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">@@ -80,9 +80,6 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineages_list</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">current_lineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{}_{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dataset_version</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">autoconfig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoConfigAuto</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">current_lineage</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The following line creates a direct reference, so whenever one analysis run adds a tool to this list it</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># is automatically updated here too.</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">autoconfig</span><span class="p">.</span><span class="n" style="color: #333;">persistent_tools</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">persistent_tools</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">busco_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">(</span><span class="n" style="color: #333;">autoconfig</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">busco_run</span><span class="p">.</span><span class="n" style="color: #333;">run_analysis</span><span class="p">(</span><span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">callback</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">root_runners</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">busco_run</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># Save all root runs so they can be recalled if chosen</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" 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="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,7 +133,7 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleanup_disused_runs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">disused_runners</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">runner</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">disused_runners</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_lineage_dataset</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: rethink structure after BuscoPlacer is finalized and protein mode with mollicutes is fixed.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="156" 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">@@ -159,14 +156,16 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Mollicutes dataset is a better match for your data. Testing subclades..."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_3_datasets</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_r<span class="idiff left">unner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">hmmer_r</span>esults_lines</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">results_datasets</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">best_match_lineage_dataset</span><span class="p">))</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="s" style="color: #d14;">"geno"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">code_4_selected</span> <span class="ow" style="font-weight: 600;">and</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">)).</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"bacteria"</span><span class="p">)):</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="s" style="color: #d14;">"geno"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">mode</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">current_gc</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"4"</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">)).</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"bacteria"</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"The results from the Prodigal gene predictor indicate that your data belongs to the "</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">"mollicutes clade. Testing subclades..."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_3_datasets</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_r<span class="idiff left">unner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">hmmer_r</span>esults_lines</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">results_datasets</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">best_match_lineage_dataset</span><span class="p">))</span></span>
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171
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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172
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_busco_placer</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">@@ -181,12 +180,12 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">runners</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_lineages_list</span><span class="p">([</span><span class="s" style="color: #d14;">"mollicutes"</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">runners</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_buscos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_buscos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_buscos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percents</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percents</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percents</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span><span class="p">)</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_buscos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">single_copy</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_buscos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">multi_copy</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_buscos</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">only_fragments</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percents</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">s_percent</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percents</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">d_percent</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percents</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">f_percent</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_best_match_lineage</span><span class="p">(</span><span class="n" style="color: #333;">runners</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC191" 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">@@ -215,12 +214,12 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_3_datasets</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">mollicutes_runner</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mollicutes_runner</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">datasets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mycoplasmatales"</span><span class="p">,</span> <span class="s" style="color: #d14;">"entomoplasmatales"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">single_copy</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">multi_copy</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">only_fragments</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">s_percent</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">d_percent</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">f_percent</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">dataset_runners</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mollicutes_runner</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC224" 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="LC225" class="line" lang="python"> <span class="n" style="color: #333;">datasets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"mollicutes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mycoplasmatales"</span><span class="p">,</span> <span class="s" style="color: #d14;">"entomoplasmatales"</span><span class="p">]</span></span>
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<li id="bf9cbed51faec015f7b0c0f8d5ec757bb662a62f">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#bf9cbed51faec015f7b0c0f8d5ec757bb662a62f"><strong>src/busco/BuscoAnalysis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,24 +4,18 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">.. module:: BuscoAnalysis</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> :synopsis: BuscoAnalysis implements general BUSCO analysis specifics</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: <span class="idiff left right">3.0.1</span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: <span class="idiff left right">4.0.7</span></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="s" style="color: #d14;">Copyright (c) 2016-2020, Evgeny Zdobnov (ez@ezlab.org)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></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;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABCMeta</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">busco</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoConfig</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoConfig</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigMain</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigAuto</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;">busco.BuscoConfig</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoConfig</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigAuto</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoTools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">HMMERRunner</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">inspect</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</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;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoLogger</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">LogDecorator</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">log</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.Toolset</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Tool</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" 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">@@ -31,115 +25,93 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> This abstract base class (ABC) defines methods required for most of BUSCO analyses and has to be extended</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"> by each specific analysis class</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> 1) load parameters</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> 2) load and validate tools</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> 3) check data and dataset integrity</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> 4) Ready for analysis</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> :param config: Values of all parameters to be used during the analysis</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> :type config: BuscoConfig</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">s<span class="idiff left">elf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_config</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">config</span></span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="nb" style="color: #0086b3;">s<span class="idiff left">uper</span></span><span class="p"><span class="idiff">().</span></span><span class="n" style="color: #333;"><span class="idiff">__init__</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get paths</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">lineage_results_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_results_dir"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># todo: decide which are hidden attributes</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">working_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto_lineage"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigAuto</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">working_dir</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">lineage_results_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"logs"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"in"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_datasets_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"datasets_version"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_results_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_results_dir"</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_working_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto_lineage"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigAuto</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_working_dir</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_results_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"logs"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get other useful variables</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">getint</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cpu"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"in"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_has_variants_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span> <span class="s" style="color: #d14;">"ancestral_variants"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_creation_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"creation_date"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_nb_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"number_of_species"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_nb_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"number_of_BUSCOs"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_creation_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"creation_date"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># Dictionary containing coordinate information for predicted genes.</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get Busco downloader</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">downloader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">downloader</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineages_download_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"download_path"</span><span class="p">),</span> <span class="s" style="color: #d14;">"lineages"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create optimized command line call for the given input</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">busco_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"main"</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigMain</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"auto"</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>self.busco_type = "main" if isinstance(self._config, BuscoConfigMain) else "auto"</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self.busco_type == "main":</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.set_rerun_busco_command(self._config.clargs) # todo: rework rerun command</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Variables storing BUSCO results</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_missing_busco_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_fragmented_busco_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># Dictionary containing coordinate information for predicted genes.</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">all_single_copy_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_count</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;"># Dummy variable used to skip logging for intermediate eukaryote pipeline results.</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: catch unicode encoding exception and report invalid character line instead of doing content validation</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># todo: check config file exists before parsing</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"></span>
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91
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">_</span>cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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93
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Delete any non-decompressed files in busco_downloads</span></span>
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94
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">dataset_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><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="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"busco_run"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"download_path"</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lineages"</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">dataset_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_lineages_download_path</span></span><span class="p">):</span></span>
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96
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dataset_name</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">((</span><span class="s" style="color: #d14;">".gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">".tar"</span><span class="p">)):</span></span>
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97
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">dataset_name</span><span class="p">)</span></span>
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98
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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99
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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100
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_data_integrity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_dataset_integrity</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">).</span><span class="n" style="color: #333;">st_size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Input file is empty."</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</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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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">):</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_fasta_header</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_checkpoint</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># TODO: rework checkpoint system</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> This function return the checkpoint if the checkpoint.tmp file exits or None if absent</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"><span class="s" style="color: #d14;"> :return: the checkpoint name</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;"> :rtype: int</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">checkpt_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">checkpoint_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"checkpoint.tmp"</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">checkpoint_file</span><span class="p">):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">checkpoint_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">check_file</span><span class="p">:</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_file</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_random</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="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;"># Reset random suffix</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">checkpt_name</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;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="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="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">checkpt_name</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Running BUSCO using lineage dataset {0} ({1}, {2})"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"_lineage_name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_domain"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_dataset_creation_date"</span><span class="p">],</span> <span class="n" style="color: #333;">on_func_exit</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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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Running BUSCO using lineage dataset {0} ({1}, {2})"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"_lineage_name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_domain"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_dataset_creation_date"</span><span class="p">],</span> <span class="n" style="color: #333;">on_func_exit</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="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> Abstract method, override to call all needed steps for running the child analysis.</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">create_dirs</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>create_dirs</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">init_tools</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_tool_dependencies</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_data_integrity</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"***** Run HMMER on gene sequences *****"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">input_sequences</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> This function runs hmmsearch.</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">files</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;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmms"</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">busco_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># Each Busco ID has a HMM file of the form "<busco_id>.hmm"</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">configure_runner</span><span class="p">(</span><span class="n" style="color: #333;">input_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">busco_ids</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span><span class="p">)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping HMMER run as output already processed"</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">process_output</span><span class="p">()</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">write_hmmer_results</span><span class="p">()</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">produce_hmmer_summary</span><span class="p">()</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></span>
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137
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Checking dataset for HMM profiles"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">debug</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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138
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_dataset_integrity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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139
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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140
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> Check the input dataset for hmm profiles, both files and folder are available</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;"> Note: score and length cutoffs are checked when read,</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;"> See _load_scores and _load_lengths</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;"> Note: score and length cutoffs are checked when read by hmmer_runner: see _load_scores and _load_lengths</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> Note: dataset.cfg file is not mandatory for offline mode</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"><span class="s" style="color: #d14;"> # todo: implement a check for dataset.cfg file if not using offline mode</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if the dataset is missing files or folders</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,18 +129,24 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"The dataset you provided lacks elements in {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span> <span class="s" style="color: #d14;">"prfl"</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># note: score and length cutoffs are checked when read,</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># see _load_scores and _load_lengths</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ancestral would cause blast to fail, and be detected, see _blast() # TODO: clarify comment</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># dataset.cfg is not mandatory</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_has_variants_file</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"The dataset you provided does not contain the file ancestral_variants, likely because it "</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="s" style="color: #d14;">"is an old version. All blast steps will use the file </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">ancestral</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_fasta_header</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_data_integrity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_dataset_integrity</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">).</span><span class="n" style="color: #333;">st_size</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 new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Input file is empty."</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_fasta_header</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_fasta_header</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">):</span></span>
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172
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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173
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> This function checks problematic characters in fasta headers,</span></span>
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174
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> and warns the user and stops the execution</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -183,7 +161,6 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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183
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="s" style="color: #d14;">"which will crash BUSCO. Please clean the header of your "</span></span>
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184
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="s" style="color: #d14;">"input file."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">char</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()))</span></span>
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185
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"></span>
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187
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">char</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">BuscoConfig</span><span class="p">.</span><span class="n" style="color: #333;">FORBIDDEN_HEADER_CHARS_BEFORE_SPLIT</span><span class="p">:</span></span>
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188
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">char</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>
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189
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -197,19 +174,7 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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197
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">></span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> which will crash Reader. Please clean the header of "</span></span>
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<td class="diff-line-num old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="s" style="color: #d14;">"your input file."</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()))</span></span>
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199
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_tool_dependencies</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> check dependencies on tools</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if a Tool version is not supported</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check hmm version</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_hmmer_version</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">BuscoConfig</span><span class="p">.</span><span class="n" style="color: #333;">HMMER_VERSION</span><span class="p">:</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="s" style="color: #d14;">"HMMer version detected is not supported, please use HMMer v.{} +"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">BuscoConfig</span><span class="p">.</span><span class="n" style="color: #333;">HMMER_VERSION</span><span class="p">))</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_dirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_create_dirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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213
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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214
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"><span class="s" style="color: #d14;"> Create the run (main) directory, log directory and the temporary directories</span></span>
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215
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" 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">@@ -223,8 +188,8 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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223
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"><span class="s" style="color: #d14;"> Create a subfolder of the main output folder that contains all log files from BUSCO and the external tools used.</span></span>
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224
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_folder</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_folder</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>log_folder</span><span class="p">):</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>log_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_create_main_dir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" 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">@@ -233,76 +198,23 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if write permissions are not available to the specified location</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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235
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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236
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>run_folder</span><span class="p">)</span></span>
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237
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">FileExistsError</span><span class="p">:</span></span>
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238
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Something went wrong. BUSCO stopped before overwriting run folder {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">))</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">:</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Something went wrong. BUSCO stopped before overwriting run folder "</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">"{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_folder</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">PermissionError</span><span class="p">:</span></span>
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240
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span></span>
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241
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="s" style="color: #d14;">"Cannot write to the output directory, please make sure "</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="s" style="color: #d14;">"you have write permissions to {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">"you have write permissions to {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>run_folder</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># @log("Temp directory is {}", logger, attr_name="_tmp", on_func_exit=True)</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def _create_tmp_dir(self):</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function creates the tmp directory</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># :raises</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># SystemExit: if the user cannot write in the tmp directory</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># try:</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not os.path.exists(self._tmp):</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># os.makedirs(self._tmp)</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># except OSError:</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># raise SystemExit(</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "Cannot write to the temp directory, please make sure "</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "you have write permissions to {}".format(self._tmp))</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return</span></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_busco_percentages</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">single_copy_buscos</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># int</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy_buscos</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># int</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">fragmented_buscos</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># int</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">cutoff_dict</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get percentage of each kind of BUSCO match</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">((</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_buscos</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;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">((</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_buscos</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;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">((</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_buscos</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;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_buscos</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_hmmer_version</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> check the Tool has the correct version</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if the version is not correct</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">hmmer_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hmmer_tool</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="s" style="color: #d14;">"-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;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;">hmmer_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmmer_version</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">"utf-8"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC284" 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="LC285" class="line" lang="python"> <span class="n" style="color: #333;">hmmer_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmmer_version</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</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;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">hmmer_version</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;">hmmer_version</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="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># to avoid a crash with a super old version</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">hmmer_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hmmer_version</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</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;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="n" style="color: #333;">hmmer_version</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;">hmmer_version</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="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hmmer_version</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Check all required tools are accessible..."</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">debug</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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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> Init the tools needed for the analysis. HMMER is needed for all BUSCO analysis types.</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC299" 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="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hmmer_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hmmer_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"hmmsearch"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"HMMer should be a tool"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HMMERRunner</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</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">@@ -310,242 +222,59 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_mode</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># @log("This is not an incomplete run that can be restarted", logger, iswarn=True)</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # Todo: decide if mini functions are necessary to facilitate decorator logging</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def _not_incomplete_run(self):</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._restart = False</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_produce_hmmer_summary</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">single_copy</span><span class="p">,</span> <span class="n" style="color: #333;">multi_copy</span><span class="p">,</span> <span class="n" style="color: #333;">only_fragments</span><span class="p">,</span> <span class="n" style="color: #333;">total_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_busco_percentages</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"***** Results: *****</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">one_line_summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"C:{}%[S:{}%,D:{}%],F:{}%,M:{}%,n:{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)),</span> <span class="n" style="color: #333;">total_buscos</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="LC326" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">one_line_summary</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</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;">Complete BUSCOs (C)</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">single_copy</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">multi_copy</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="LC328" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</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;">Complete and single-copy BUSCOs (S)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">single_copy</span><span class="p">,</span> <span class="s" style="color: #d14;">" "</span><span class="p">))</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</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;">Complete and duplicated BUSCOs (D)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">multi_copy</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="LC330" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</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;">Fragmented BUSCOs (F)</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">only_fragments</span><span class="p">,</span> <span class="s" style="color: #d14;">" "</span><span class="p">))</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</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;">Missing BUSCOs (M)</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">total_buscos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">single_copy</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">multi_copy</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">only_fragments</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="LC333" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</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;">Total BUSCO groups searched</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">total_buscos</span><span class="p">,</span> <span class="s" style="color: #d14;">" "</span><span class="p">))</span></span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"></span>
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335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"short_summary.txt"</span><span class="p">),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">summary_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_output_header</span><span class="p">(</span><span class="n" style="color: #333;">summary_file</span><span class="p">,</span> <span class="n" style="color: #333;">no_table_header</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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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">summary_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Summarized benchmarking in BUSCO notation for file {}</span><span class="se" style="color: #d14;">\n</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="225" 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="s" style="color: #d14;">"# BUSCO was run in mode: {}</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span><span class="p">))</span></span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">:</span></span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">summary_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">))</span></span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"></span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigMain</span><span class="p">)</span> \</span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">,</span> <span class="s" style="color: #d14;">"placement_files"</span><span class="p">):</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">summary_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Placement file versions:</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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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">placement_file</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">placement_files</span><span class="p">:</span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">summary_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">placement_file</span><span class="p">))</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"></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;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigAuto</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: rework this if/else block</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_one_line_hmmer_summary</span><span class="p">()</span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"eukaryota"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_count</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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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_log_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_produce_full_hmmer_summary_debug</span><span class="p">()</span></span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_one_line_hmmer_summary</span><span class="p">()</span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"></span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"{}"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"hmmer_results_lines"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">apply</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"join"</span><span class="p">,</span> <span class="n" style="color: #333;">on_func_exit</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="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_produce_full_hmmer_summary</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="k" style="font-weight: 600;">return</span></span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"{}"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"hmmer_results_lines"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">apply</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"join"</span><span class="p">,</span> <span class="n" style="color: #333;">on_func_exit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">debug</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="LC365" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_produce_full_hmmer_summary_debug</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"{}"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"one_line_summary"</span><span class="p">,</span> <span class="n" style="color: #333;">on_func_exit</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="LC369" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_one_line_hmmer_summary</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">one_line_summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Results:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">one_line_summary</span><span class="p">)</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"***** Run HMMER on gene sequences *****"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">input_sequences</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"><span class="s" style="color: #d14;"> This function runs hmmsearch.</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hmmer_tool</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hmmer_tool</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">hmmer_output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmmer_output"</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">hmmer_output_dir</span><span class="p">):</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">hmmer_output_dir</span><span class="p">)</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">files</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;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmms"</span><span class="p">)))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="385" 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">
385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">busco_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># Each Busco ID has a HMM file of the form "<busco_id>.hmm"</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HMMERRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_hmmer_tool</span><span class="p">,</span> <span class="n" style="color: #333;">input_sequences</span><span class="p">,</span> <span class="n" style="color: #333;">busco_ids</span><span class="p">,</span> <span class="n" style="color: #333;">hmmer_output_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gene_details</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_datasets_version</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">load_buscos</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">process_output</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.all_single_copy_buscos.update(self.hmmer_runner.single_copy_buscos)</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_hmmer_results</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_produce_hmmer_summary</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_write_buscos_to_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">sequences_aa</span><span class="p">,</span> <span class="n" style="color: #333;">sequences_nt</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"><span class="s" style="color: #d14;"> Write BUSCO matching sequences to output fasta files. Each sequence is printed in a separate file and both</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"><span class="s" style="color: #d14;"> nucleotide and amino acid versions are created.</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"><span class="s" style="color: #d14;"> :param busco_type: one of ["single_copy", "multi_copy", "fragmented"]</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">busco_type</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"single_copy"</span><span class="p">,</span> <span class="s" style="color: #d14;">"multi_copy"</span><span class="p">,</span> <span class="s" style="color: #d14;">"fragmented"</span><span class="p">]:</span></span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"single_copy"</span><span class="p">:</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"busco_sequences"</span><span class="p">,</span> <span class="s" style="color: #d14;">"single_copy_busco_sequences"</span><span class="p">)</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">busco_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">single_copy_buscos</span></span>
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<td class="diff-line-num old old_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">busco_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"multi_copy"</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="409" 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">
409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"busco_sequences"</span><span class="p">,</span> <span class="s" style="color: #d14;">"multi_copy_busco_sequences"</span><span class="p">)</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">busco_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy_buscos</span></span>
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<td class="diff-line-num old old_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">busco_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fragmented"</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;">output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"busco_sequences"</span><span class="p">,</span> <span class="s" style="color: #d14;">"fragmented_busco_sequences"</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="413" 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">
413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">busco_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">fragmented_buscos</span></span>
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<td class="diff-line-num old old_line" data-linenumber="414" 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">
414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: move all create_dir commands to one place</span></span>
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<td class="diff-line-num old old_line" data-linenumber="416" 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">
416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">)</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"></span>
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418
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">busco</span><span class="p">,</span> <span class="n" style="color: #333;">gene_matches</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">busco_matches</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">aa_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">nt_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">[(</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">],</span> <span class="n" style="color: #333;">sequences_nt</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gene_matches</span><span class="p">])</span></span>
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<td class="diff-line-num old old_line" data-linenumber="421" 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">
421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.fna"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">busco</span><span class="p">)),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f2</span><span class="p">:</span></span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">nt_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">f2</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="423" 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">
423
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">:</span></span>
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424
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">aa_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">[</span><span class="n" style="color: #333;">gene_id</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gene_matches</span><span class="p">]</span></span>
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425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.faa"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">busco</span><span class="p">)),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">aa_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def _run_tarzip_hmmer_output(self): # todo: rewrite using tarfile</span></span>
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431
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function tarzips "hmmer_output" results folder</span></span>
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433
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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434
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._p_open(["tar", "-C", "%s" % self.run_folder, "-zcf", "%shmmer_output.tar.gz" % self.run_folder,</span></span>
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435
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "hmmer_output", "--remove-files"], "bash", shell=False)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># @log("To reproduce this run: {}", logger, attr_name="_rerun_cmd", on_func_exit=True)</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def set_rerun_busco_command(self, clargs): # todo: reconfigure</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function sets the command line to call to reproduce this run</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # Find python script path</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># entry_point = ""</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># frame_ind = -1</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># while "run_BUSCO.py" not in entry_point:</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># entry_point = inspect.stack()[frame_ind].filename</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># frame_ind -= 1</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # Add required parameters and other options</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd = "python %s -i %s -o %s -l %s -m %s -c %s" % (entry_point, self._input_file, os.path.basename(self.main_out),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._lineage_dataset, self._mode, self._cpus)</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># try:</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._long:</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd += " --long"</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._region_limit != BuscoConfig.DEFAULT_ARGS_VALUES["limit"]:</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd += " --limit %s" % self._region_limit</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # if self._tmp != BuscoConfig.DEFAULT_ARGS_VALUES["tmp_path"]:</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # self._rerun_cmd += " -t %s" % self._tmp</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._ev_cutoff != BuscoConfig.DEFAULT_ARGS_VALUES["evalue"]:</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd += " -e %s" % self._ev_cutoff</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # if self._tarzip:</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # self._rerun_cmd += " -z"</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># except AttributeError:</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pass</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # Include any command line arguments issued by the user</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # arg_aliases = {"-i": "--in", "-o": "--out", "-l": "--lineage_dataset", "-m": "--mode", "-c": "--cpu",</span></span>
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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # "-e": "--evalue", "-f": "--force", "-sp": "--species", "-z": "--tarzip",</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # "-r": "--restart", "-q": "--quiet", "-v": "--version", "-h": "--help"}</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># arg_aliases.update(dict(zip(arg_aliases.values(), arg_aliases.keys())))</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for a, arg in enumerate(clargs):</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if arg.startswith("-") and not arg in self._rerun_cmd:</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if arg in arg_aliases:</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if arg_aliases[arg] in self._rerun_cmd:</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># continue</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if a + 1 < len(clargs) and not clargs[a + 1].startswith("-"):</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd += " %s %s" % (arg, clargs[a + 1])</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># else:</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd += " %s" % arg</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return</span></span>
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436
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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437
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"></span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"></span>
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439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"To reproduce this run: {}"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"_rerun_cmd"</span><span class="p">,</span> <span class="n" style="color: #333;">on_func_exit</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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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_rerun_busco_command</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">clargs</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: reconfigure</span></span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"><span class="s" style="color: #d14;"> This function sets the command line to call to reproduce this run</span></span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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444
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"></span>
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445
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Find python script path</span></span>
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446
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">entry_point</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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447
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">frame_ind</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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448
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="s" style="color: #d14;">"run_BUSCO.py"</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;">entry_point</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;">entry_point</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inspect</span><span class="p">.</span><span class="n" style="color: #333;">stack</span><span class="p">()[</span><span class="n" style="color: #333;">frame_ind</span><span class="p">].</span><span class="n" style="color: #333;">filename</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">frame_ind</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="LC451" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add required parameters and other options</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"python %s -i %s -o %s -l %s -m %s -c %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">entry_point</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC456" 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="LC457" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_long</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" --long"</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_region_limit</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">BuscoConfig</span><span class="p">.</span><span class="n" style="color: #333;">DEFAULT_ARGS_VALUES</span><span class="p">[</span><span class="s" style="color: #d14;">"limit"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" --limit %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_region_limit</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._tmp != BuscoConfig.DEFAULT_ARGS_VALUES["tmp_path"]:</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd += " -t %s" % self._tmp</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ev_cutoff</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">BuscoConfig</span><span class="p">.</span><span class="n" style="color: #333;">DEFAULT_ARGS_VALUES</span><span class="p">[</span><span class="s" style="color: #d14;">"evalue"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" -e %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ev_cutoff</span></span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._tarzip:</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._rerun_cmd += " -z"</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Include any command line arguments issued by the user</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># arg_aliases = {"-i": "--in", "-o": "--out", "-l": "--lineage_dataset", "-m": "--mode", "-c": "--cpu",</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "-e": "--evalue", "-f": "--force", "-sp": "--species", "-z": "--tarzip",</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "-r": "--restart", "-q": "--quiet", "-v": "--version", "-h": "--help"}</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">arg_aliases</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">arg_aliases</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">arg_aliases</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())))</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">clargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">arg_aliases</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;">if</span> <span class="n" style="color: #333;">arg_aliases</span><span class="p">[</span><span class="n" style="color: #333;">arg</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">clargs</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clargs</span><span class="p">[</span><span class="n" style="color: #333;">a</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;">startswith</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="LC481" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" %s %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="n" style="color: #333;">clargs</span><span class="p">[</span><span class="n" style="color: #333;">a</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="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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_cmd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">arg</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_write_hmmer_results</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> <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="s" style="color: #d14;"> Create two output files: one with information on all BUSCOs for the given dataset and the other with a list of</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"><span class="s" style="color: #d14;"> all BUSCOs that were not found.</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"full_table.tsv"</span><span class="p">),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f_out</span><span class="p">:</span></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">output_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">_create_output_content</span><span class="p">()</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_output_header</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"missing_busco_list.tsv"</span><span class="p">),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">miss_out</span><span class="p">:</span></span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_output_header</span><span class="p">(</span><span class="n" style="color: #333;">miss_out</span><span class="p">,</span> <span class="n" style="color: #333;">missing_list</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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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="python"> <span class="n" style="color: #333;">missing_buscos_lines</span><span class="p">,</span> <span class="n" style="color: #333;">missing_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">_list_missing_buscos</span><span class="p">()</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">output_lines</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">missing_buscos_lines</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">missing_busco</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">missing_buscos</span><span class="p">):</span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">miss_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">missing_busco</span><span class="p">))</span></span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">sorted_output_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_sort_lines</span><span class="p">(</span><span class="n" style="color: #333;">output_lines</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="509" 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">
509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">busco</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sorted_output_lines</span><span class="p">:</span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">f_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">busco</span><span class="p">)</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_sort_lines</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">sorted_lines</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;">lines</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"at"</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="LC516" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sorted_lines</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_write_output_header</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_object</span><span class="p">,</span> <span class="n" style="color: #333;">missing_list</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">no_table_header</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="LC522" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"><span class="s" style="color: #d14;"> Write a standardized file header containing information on the BUSCO run.</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"><span class="s" style="color: #d14;"> :param file_object: Opened file object ready for writing</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"><span class="s" style="color: #d14;"> :type file_object: file</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"> <span class="n" style="color: #333;">file_object</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# BUSCO version is: {} </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="LC529" class="line" lang="python"> <span class="s" style="color: #d14;">"# The lineage dataset is: {} (Creation date: {}, number of species: {}, number of BUSCOs: {}"</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"> <span class="s" style="color: #d14;">")</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">busco</span><span class="p">.</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_creation_date</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_nb_species</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_dataset_nb_buscos</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if isinstance(self._config, BuscoConfigMain): # todo: wait until rerun command properly implemented again</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># file_object.write("# To reproduce this run: {}\n#\n".format(self._rerun_cmd))</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">no_table_header</span><span class="p">:</span></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">missing_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">file_object</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Busco id</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="LC539" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"proteins"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"transcriptome"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">extra_columns</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">file_object</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Busco id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Status</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Sequence</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">OrthoDB url</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Description</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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542
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<pre style="margin: 0;">-<span id="LC542" 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="LC543" class="line" lang="python"> <span class="n" style="color: #333;">file_object</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Busco id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Status</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Sequence</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Length</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="LC544" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"genome"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">extra_columns</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="python"> <span class="n" style="color: #333;">file_object</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Busco id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Status</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Sequence</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Gene Start</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Gene End</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Length</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">OrthoDB url</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Description</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="LC547" 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="LC548" class="line" lang="python"> <span class="n" style="color: #333;">file_object</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Busco id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Status</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Sequence</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Gene Start</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Gene End</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Length</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="LC549" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"></span></pre>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: catch unicode encoding exception and report invalid character line instead of doing content validation</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;"># todo: check config file exists before parsing</span></span></pre>
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<li id="e497bbf996017c0692c161d2cfed28374276cc73">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#e497bbf996017c0692c161d2cfed28374276cc73"><strong>src/busco/BuscoConfig.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,7 @@ logger = BuscoLogger.get_logger(__name__)</td>
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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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BaseConfig</span><span class="p">(</span><span class="n" style="color: #333;">ConfigParser</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_ARGS_VALUES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"out_path"</span><span class="p">:</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">(),</span> <span class="s" style="color: #d14;">"cpu"</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"force"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">"evalue"</span><span class="p">:</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">DEFAULT_ARGS_VALUES</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"out_path"</span><span class="p">:</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">(),</span> <span class="s" style="color: #d14;">"cpu"</span><span class="p">:</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"force"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">"<span class="idiff left">restart"</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>evalue"</span><span class="p">:</span> <span class="mf" style="color: #099;">1e-3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"limit"</span><span class="p">:</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">"long"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">"quiet"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"download_path"</span><span class="p">:</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">(),</span> <span class="s" style="color: #d14;">"busco_downloads"</span><span class="p">),</span> <span class="s" style="color: #d14;">"datasets_version"</span><span class="p">:</span> <span class="s" style="color: #d14;">"odb10"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"offline"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">"download_base_url"</span><span class="p">:</span> <span class="s" style="color: #d14;">"https://busco-data.ezlab.org/v4/data/"</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">@@ -49,6 +49,10 @@ class BaseConfig(ConfigParser):</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">downloader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoDownloadManager</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># @log("Setting value in config")</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def set(self, *args, **kwargs):</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># super().set(*args, **kwargs)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PseudoConfig</span><span class="p">(</span><span class="n" style="color: #333;">BaseConfig</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC58" 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">@@ -200,9 +204,10 @@ class BuscoConfigMain(BuscoConfig, BaseConfig):</td>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">MANDATORY_USER_PROVIDED_PARAMS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"in"</span><span class="p">,</span> <span class="s" style="color: #d14;">"out"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">CONFIG_STRUCTURE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"in"</span><span class="p">,</span> <span class="s" style="color: #d14;">"out"</span><span class="p">,</span> <span class="s" style="color: #d14;">"out_path"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage-prok"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="s" style="color: #d14;">"auto-lineage-euk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cpu"</span><span class="p">,</span> <span class="s" style="color: #d14;">"force"</span><span class="p">,</span> <span class="s" style="color: #d14;">"download_path"</span><span class="p">,</span> <span class="s" style="color: #d14;">"datasets_version"</span><span class="p">,</span> <span class="s" style="color: #d14;">"evalue"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="s" style="color: #d14;">"limit"</span><span class="p">,</span> <span class="s" style="color: #d14;">"long"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span> <span class="s" style="color: #d14;">"offline"</span><span class="p">,</span> <span class="s" style="color: #d14;">"download_base_url"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">,</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">"update-data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_parameters"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_species"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">],</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">"auto-lineage-euk"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cpu"</span><span class="p">,</span> <span class="s" style="color: #d14;">"force"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="s" style="color: #d14;">"download_path"</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="s" style="color: #d14;">"datasets_version"</span><span class="p">,</span> <span class="s" style="color: #d14;">"evalue"</span><span class="p">,</span> <span class="s" style="color: #d14;">"limit"</span><span class="p">,</span> <span class="s" style="color: #d14;">"long"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span> <span class="s" style="color: #d14;">"offline"</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">"download_base_url"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">,</span> <span class="s" style="color: #d14;">"update-data"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_parameters"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="s" style="color: #d14;">"augustus_species"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">],</span></span>
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="s" style="color: #d14;">"tblastn"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"path"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command"</span><span class="p">],</span></span>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="s" style="color: #d14;">"makeblastdb"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"path"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command"</span><span class="p">],</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="s" style="color: #d14;">"prodigal"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"path"</span><span class="p">,</span> <span class="s" style="color: #d14;">"command"</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">@@ -241,7 +246,6 @@ class BuscoConfigMain(BuscoConfig, BaseConfig):</td>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_required_input_exists</span><span class="p">()</span></span>
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"></span>
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243
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_init_downloader</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">persistent_tools</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"></span>
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_config</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC251" 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">@@ -259,7 +263,7 @@ class BuscoConfigMain(BuscoConfig, BaseConfig):</td>
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259
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">lineage_dataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">)</span></span>
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260
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">datasets_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"datasets_version"</span><span class="p">)</span></span>
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261
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"_odb"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineage_dataset</span><span class="p">:</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">dataset_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage_dataset</span><span class="p">.</span><span class="n" style="color: #333;">rsplit</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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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">dataset_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage_dataset</span><span class="p">.</span><span class="n" style="color: #333;">rsplit</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 class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</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 right">)</span></span></span>
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263
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">datasets_version</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">dataset_version</span><span class="p">:</span></span>
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264
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"There is a conflict in your config. You specified a dataset from {0} while "</span></span>
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265
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="s" style="color: #d14;">"simultaneously requesting the datasets_version parameter be {1}. Proceeding with "</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="368" 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="372" 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">@@ -368,11 +372,15 @@ class BuscoConfigMain(BuscoConfig, BaseConfig):</td>
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368
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">):</span></span>
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369
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"force"</span><span class="p">):</span></span>
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370
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_force_remove_existing_output_dir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">)</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">):</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Attempting to restart the run using the following directory: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">))</span></span>
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371
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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372
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"A run with the name {} already exists...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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373
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">If you are sure you wish to overwrite existing files, "</span></span>
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374
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="s" style="color: #d14;">"please use the -f (force) option"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Restart mode not available as directory {} does not exist."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">))</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="s" style="color: #d14;">"False"</span><span class="p">)</span></span>
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376
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"></span>
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377
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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378
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"></span>
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<li id="187e8b3b00a66c92055c44aac0cd5c916c6c913e">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#187e8b3b00a66c92055c44aac0cd5c916c6c913e"><strong>src/busco/BuscoDownloadManager.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,7 +50,8 @@ class BuscoDownloadManager:</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_create_main_download_dir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">):</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># exist_ok=True to allow for multiple parallel BUSCO runs each trying to create this folder simultaneously</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">,</span> <span class="n" style="color: #333;">exist_ok</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="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_load_versions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="83" 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="84" 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">@@ -83,7 +84,8 @@ class BuscoDownloadManager:</td>
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83
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if the category folder does not exist, create it</span></span>
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84
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">category_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">,</span> <span class="n" style="color: #333;">category</span><span class="p">)</span></span>
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85
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">category_folder</span><span class="p">):</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">category_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># exist_ok=True to allow for multiple parallel BUSCO runs, each trying to create this folder</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">category_folder</span><span class="p">,</span> <span class="n" style="color: #333;">exist_ok</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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87
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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88
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"></span>
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89
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" 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">@@ -100,7 +102,10 @@ class BuscoDownloadManager:</td>
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100
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dataset_date</span></span>
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101
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"></span>
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102
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_existing_version</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="n" style="color: #333;">category</span><span class="p">,</span> <span class="n" style="color: #333;">data_basename</span><span class="p">):</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">latest_update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">version_files</span><span class="p">[</span><span class="n" style="color: #333;">data_basename</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">latest_update</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">version_files</span><span class="p">[</span><span class="n" style="color: #333;">data_basename</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"{} is not a valid option for '{}'"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">data_basename</span><span class="p">,</span> <span class="n" style="color: #333;">category</span><span class="p">))</span></span>
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104
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">path_basename</span><span class="p">,</span> <span class="n" style="color: #333;">extension</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">data_basename</span><span class="p">)</span></span>
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105
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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106
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">category</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"lineages"</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" 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="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -136,19 +141,22 @@ class BuscoDownloadManager:</td>
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136
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">local_dataset</span><span class="p">):</span></span>
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137
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">local_dataset</span></span>
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138
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to run BUSCO in offline mode. Dataset {} does not exist."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">local_dataset</span><span class="p">))</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to run BUSCO in offline mode. Dataset {} does not "</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"exist."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">local_dataset</span><span class="p">))</span></span>
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140
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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141
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">basename</span><span class="p">,</span> <span class="n" style="color: #333;">extension</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">data_name</span><span class="p">)</span></span>
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142
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">placement_files</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;">glob</span><span class="p">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span></span>
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143
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">,</span> <span class="n" style="color: #333;">category</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.*{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">basename</span><span class="p">,</span> <span class="n" style="color: #333;">extension</span><span class="p">))))</span></span>
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144
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<td class="diff-line-num new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;"> <span id="LC150" 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;">placement_files</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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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">placement_files</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;"># todo: for offline mode, log which files are being used (in case of more than one glob match)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">placement_files</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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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># todo: for offline mode, log which files are being used (in case of more than one glob match)</span></span>
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146
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to run BUSCO placer in offline mode. Cannot find necessary placement files in {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">))</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to run BUSCO placer in offline mode. Cannot find necessary placement "</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">"files in {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">))</span></span>
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148
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">data_basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">data_name</span><span class="p">)</span></span>
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149
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">local_filepath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">local_download_path</span><span class="p">,</span> <span class="n" style="color: #333;">category</span><span class="p">,</span> <span class="n" style="color: #333;">data_basename</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="n" style="color: #333;">up_to_date</span><span class="p">,</span> <span class="n" style="color: #333;">latest_version</span><span class="p">,</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_existing_version</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">local_filepath</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">category</span></span><span class="p"><span class="idiff right">,</span></span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="idiff left right"> </span> <span class="n" style="color: #333;">data_basename</span><span class="p">)</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">present</span><span class="p">,</span> <span class="n" style="color: #333;">up_to_date</span><span class="p">,</span> <span class="n" style="color: #333;">latest_version</span><span class="p">,</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_existing_version</span><span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">local_filepath</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">category</span></span><span class="p"><span class="idiff right">,</span></span> <span class="n" style="color: #333;">data_basename</span><span class="p">)</span></span>
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152
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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153
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">up_to_date</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">update_data</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">present</span><span class="p">:</span></span>
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154
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># download</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" 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="177" 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">@@ -169,7 +177,8 @@ class BuscoDownloadManager:</td>
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169
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"></span>
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170
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">local_filepath</span></span>
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171
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_rename_old_version</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">):</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_rename_old_version</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">):</span></span>
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173
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">):</span></span>
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174
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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175
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.old"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -179,7 +188,7 @@ class BuscoDownloadManager:</td>
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179
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">timestamp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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180
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.old.{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="n" style="color: #333;">timestamp</span><span class="p">))</span></span>
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181
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Renaming {} into {}.old.{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">,</span> <span class="n" style="color: #333;">timestamp</span><span class="p">))</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">e</span></span><span class="p">:</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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183
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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184
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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185
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,7 +198,8 @@ class BuscoDownloadManager:</td>
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189
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<td class="diff-line-num new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">urllib</span><span class="p">.</span><span class="n" style="color: #333;">request</span><span class="p">.</span><span class="n" style="color: #333;">urlretrieve</span><span class="p">(</span><span class="n" style="color: #333;">remote_filepath</span><span class="p">,</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">)</span></span>
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190
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<td class="diff-line-num new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">observed_hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">_md5</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">)</span></span>
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191
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">observed_hash</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">expected_hash</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"md5 hash is incorrect: {} while {} expected"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">observed_hash</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">expected_hash</span><span class="p">)))</span></span>
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<td class="diff-line-num new old_line" data-linenumber="193" 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="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"md5 hash is incorrect: {} while {} expected"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">observed_hash</span><span class="p">),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">expected_hash</span><span class="p">)))</span></span>
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193
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"deleting corrupted file {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">))</span></span>
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194
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">local_filepath</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"BUSCO was unable to download or update all necessary files"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="218" 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">@@ -208,7 +218,6 @@ class BuscoDownloadManager:</td>
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208
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">hash_md5</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">)</span></span>
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209
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hash_md5</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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210
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"></span>
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212
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Decompressing file {}"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">func_arg</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="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_decompress_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">):</span></span>
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214
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">unzipped_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">local_filepath</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<li id="ea2771659c3ac27a7eedddf367d04f0deb13246b">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#ea2771659c3ac27a7eedddf367d04f0deb13246b"><strong>src/busco/BuscoLogger.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,11 +83,12 @@ class LogDecorator:</td>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"></span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">string_arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">obj_inst</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attr_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># string_arg = attr</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'join'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">string_arg</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">string_arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">string_arg</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># Ensure all parameters are joinable strings</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">string_arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">string_arg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">apply</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"basename"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">string_arg</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">string_arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">string_arg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">log_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">msg</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">string_arg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># if there are multiple attributes specified</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">string_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">obj_inst</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">attr</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attr_name</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" 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">@@ -247,10 +248,14 @@ class BuscoLogger(logging.getLoggerClass()):</td>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_err_hdlr</span><span class="p">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_normal_formatter</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_err_hdlr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">(),</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">W_OK</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"No permission to write in the current directory."</span><span class="p">)</span></span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Random id used in filename to avoid complications for parallel BUSCO runs.</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">FileHandler</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_{}.log"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">random_id</span><span class="p">),</span> <span class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC251" 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="LC252" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Random id used in filename to avoid complications for parallel BUSCO runs.</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">FileHandler</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_{}.log"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">random_id</span><span class="p">),</span> <span class="n" style="color: #333;">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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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">errStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"No permission to write in the current directory: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getcwd</span><span class="p">())</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">13</span> \</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"IO error({0}): {1}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">errno</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">strerror</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="n" style="color: #333;">errStr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"></span>
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span><span class="p">.</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span><span class="p">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_verbose_formatter</span><span class="p">)</span></span>
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span><span class="p">)</span></span>
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<li id="414e3994e90f7a52298faa998003b76c548435da">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#414e3994e90f7a52298faa998003b76c548435da"><strong>src/busco/BuscoPlacer.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,9 +35,13 @@ class BuscoPlacer:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cpu"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_folder</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">placement_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"placement_files"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">placement_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">placement_folder</span><span class="p">,</span> <span class="n" style="color: #333;">exist_ok</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="LC43" 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="LC44" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">placement_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">downloader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">downloader</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">datasets_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"datasets_version"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">protein_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protein_seqs</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">@@ -92,12 +96,14 @@ class BuscoPlacer:</td>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dataset</span><span class="p">,</span> <span class="n" style="color: #333;">placement_file_versions</span></span>
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93
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_sepp</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_sepp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"sepp"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"SEPP should be a tool"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">SEPPRunner</span><span class="p">,</span> <span class="s" style="color: #d14;">"config"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sepp_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SEPPRunner</span><span class="p">()</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># try:</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assert isinstance(self._sepp, Tool)</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># except AttributeError:</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._sepp = Tool("sepp", self._config)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># except AssertionError:</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># raise SystemExit("SEPP should be a tool")</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_pick_dataset</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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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">@@ -273,10 +279,16 @@ class BuscoPlacer:</td>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Place the markers on the reference tree..."</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_sepp</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sepp_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SEPPRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_sepp</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">placement_folder</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree_nwk_file</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree_metadata_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">supermatrix_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">downloader</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">datasets_version</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cpus</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sepp_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.sepp_runner = SEPPRunner(self._sepp, self.run_folder, self.placement_folder, self.tree_nwk_file,</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.tree_metadata_file, self.supermatrix_file, self.downloader,</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.datasets_version, self.cpus)</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sepp_runner</span><span class="p">.</span><span class="n" style="color: #333;">configure_runner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree_nwk_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tree_metadata_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">supermatrix_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">downloader</span><span class="p">)</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sepp_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping SEPP run as it has already been completed"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC288" 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="LC289" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sepp_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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280
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"></span>
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281
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_extract_marker_sequences</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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282
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#a8fd6f8fc327bd92758f2c1e85bd45f1bad18df0"><strong>src/busco/BuscoRunner.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoAnalysis</span></span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.GenomeAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GenomeAnalysisEukaryotes</span></span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.TranscriptomeAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TranscriptomeAnalysis</span></span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.GeneSetAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GeneSetAnalysis</span></span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.GenomeAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GenomeAnalysisProkaryotes</span></span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoLogger</span></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoConfig</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoConfigMain</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoTools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NoGenesError</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoTools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NoGenesError</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">BaseRunner</span></span></span>
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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">configparser</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NoOptionError</span></span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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12
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BuscoRunner</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">mode_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"euk_genome"</span><span class="p">:</span> <span class="n" style="color: #333;">GenomeAnalysisEukaryotes</span><span class="p">,</span> <span class="s" style="color: #d14;">"prok_genome"</span><span class="p">:</span> <span class="n" style="color: #333;">GenomeAnalysisProkaryotes</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">@@ -23,6 +25,8 @@ class BuscoRunner:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">BaseRunner</span><span class="p">,</span> <span class="s" style="color: #d14;">"config"</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">,</span> <span class="s" style="color: #d14;">"config"</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mode"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain"</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">@@ -33,25 +37,24 @@ class BuscoRunner:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">domain</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"euk_genome"</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">analysis_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">mode_dict</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">analysis_type</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">config</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">analysis_type</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prok_fail_count</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;"># Needed to check if both bacteria and archaea return no genes.</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">callback</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">:</span> <span class="bp" style="color: #999;">None</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;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">s_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">d_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">f_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">d_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">f_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigMain</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">_cleanup</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;">s_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">d_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">f_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">d_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">f_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">NoGenesError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">nge</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">no_genes_msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"{0} did not recognize any genes matching the dataset {1} in the input file. "</span> \</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"If this is unexpected, check your input file and your <span class="idiff left">installation of {0}</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">nge</span><span class="p">.</span><span class="n" style="color: #333;">gene_predictor</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"If this is unexpected, check your input file and your <span class="idiff left">"</span></span><span class="idiff right"> \</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"installation of {0}</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">nge</span><span class="p">.</span><span class="n" style="color: #333;">gene_predictor</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">fatal</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoConfigMain</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage-euk"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"euk_genome"</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage-prok"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"prok_genome"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" 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">@@ -62,11 +65,10 @@ class BuscoRunner:</td>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="n" style="color: #333;">no_genes_msg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">s_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"prok_genome"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">persistent_tools</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prok_fail_count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">SystemExit</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">se</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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70
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">se</span></span>
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71
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">s_buscos</span><span class="p">,</span> <span class="n" style="color: #333;">d_buscos</span><span class="p">,</span> <span class="n" style="color: #333;">f_buscos</span><span class="p">,</span> <span class="n" style="color: #333;">s_percent</span><span class="p">,</span> <span class="n" style="color: #333;">d_percent</span><span class="p">,</span> <span class="n" style="color: #333;">f_percent</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;"> <span id="LC74" 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">@@ -96,14 +98,16 @@ class BuscoRunner:</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">missing_in_parasitic_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">entry</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">entry</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parasitic_file</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()]</span></span>
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<pre style="margin: 0;"> <span id="LC99" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">missing_buscos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">0.8</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_in_parasitic_buscos</span><span class="p">)</span> \</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <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;">missing_in_parasitic_buscos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">intersection</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mb</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">missing_buscos</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_in_parasitic_buscos</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">percent_missing_in_parasites</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">intersection</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">missing_buscos</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="LC101" class="line" lang="python"> <span class="n" style="color: #333;">intersection</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mb</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">missing_buscos</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mb</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_in_parasitic_buscos</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">percent_missing_in_parasites</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">intersection</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">missing_buscos</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="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">percent_missing_in_parasites</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">80.0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">corrected_summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_recalculate_parasitic_scores</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_in_parasitic_buscos</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">positive_parasitic_line</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;">!!! The missing BUSCOs match the pattern of a parasitic-reduced "</span> \</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">"genome. {}% of your missing BUSCOs are typically missing in these. "</span> \</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="s" style="color: #d14;">"A corrected score would be: </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">percent_missing_in_parasites</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">corrected_summary</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">corrected_summary</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">final_output_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">positive_parasitic_line</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage"</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">auto_lineage_line</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;">Consider using the auto-lineage mode to select a more specific lineage."</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">@@ -115,28 +119,29 @@ class BuscoRunner:</td>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">final_output_results</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_recalculate_parasitic_scores</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">num_missing_in_parasitic</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">total_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">total_buscos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">num_missing_in_parasitic</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">single_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">single_copy</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">multi_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">fragmented_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">total_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">total_buscos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">num_missing_in_parasitic</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">single_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">single_copy</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">multi_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">multi_copy</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">fragmented_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">only_fragments</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">single_copy</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">total_buscos</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="LC127" class="line" lang="python"> <span class="n" style="color: #333;">d_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">multi_copy</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">total_buscos</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="LC128" class="line" lang="python"> <span class="n" style="color: #333;">f_percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fragmented_copy</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">total_buscos</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="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">one_line_summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"C:{}%[S:{}%,D:{}%],F:{}%,M:{}%,n:{}</span><span class="se" style="color: #d14;">\t\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d_percent</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">s_percent</span><span class="p">,</span> <span class="n" style="color: #333;">d_percent</span><span class="p">,</span> <span class="n" style="color: #333;">f_percent</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s_percent</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">d_percent</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">f_percent</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">total_buscos</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">s_percent</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d_percent</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">s_percent</span><span class="p">,</span> <span class="n" style="color: #333;">d_percent</span><span class="p">,</span> <span class="n" style="color: #333;">f_percent</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">s_percent</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">d_percent</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">f_percent</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">total_buscos</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">one_line_summary</span></span>
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">organize_final_output</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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133
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">main_out_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">)</span></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">domain_results_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"domain_run_name"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">root_domain_output_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto_lineage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"run_{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">domain_results_folder</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">root_domain_output_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto_lineage"</span><span class="p">,</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">"run_{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">domain_results_folder</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">root_domain_output_folder_final</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"run_{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">domain_results_folder</span><span class="p">))</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">root_domain_output_folder</span><span class="p">,</span> <span class="n" style="color: #333;">root_domain_output_folder_final</span><span class="p">)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">symlink</span><span class="p">(</span><span class="n" style="color: #333;">root_domain_output_folder_final</span><span class="p">,</span> <span class="n" style="color: #333;">root_domain_output_folder</span><span class="p">)</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">copyfile</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">root_domain_output_folder_final</span><span class="p">,</span> <span class="s" style="color: #d14;">"short_summary.txt"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"short_summary.generic.{}.{}.txt"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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142
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">domain_results_folder</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"run_"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">),</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">))))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -155,8 +160,10 @@ class BuscoRunner:</td>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">lineage_results_folder</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"run_"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">),</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">))))</span></span>
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156
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># This is deliberately a staticmethod so it can be called from run_BUSCO() even if BuscoRunner has not yet been initialized.</span></span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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159
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">move_log_file</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This is deliberately a staticmethod so it can be called from run_BUSCO() even if BuscoRunner has not yet</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># been initialized.</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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161
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">log_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">),</span> <span class="s" style="color: #d14;">"logs"</span><span class="p">)</span></span>
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162
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">log_folder</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,11 +173,7 @@ class BuscoRunner:</td>
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166
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to move 'busco_{}.log' to the 'logs' folder."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">random_id</span><span class="p">))</span></span>
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167
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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168
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">finish</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">elapsed_time</span><span class="p">,</span> <span class="n" style="color: #333;">root_lineage</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if root_lineage:</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># logger.info("Generic lineage selected. Results reproduced here.\n"</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "{}".format(" ".join(self.analysis.hmmer_results_lines)))</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">finish</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">elapsed_time</span><span class="p">):</span></span>
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174
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"></span>
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175
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">final_output_results</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">format_results</span><span class="p">()</span></span>
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176
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">final_output_results</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="268" 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">@@ -265,5 +268,3 @@ class SmartBox:</td>
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265
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">box_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">))</span></span>
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">box_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">add_horizontal</span><span class="p">()))</span></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">box_lines</span><span class="p">)</span></span></pre>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"></span></pre>
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<li id="200a2d1cfa2fb65158ca0f851c48c1054f174e7a">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#200a2d1cfa2fb65158ca0f851c48c1054f174e7a"><strong>src/busco/BuscoTools.py</strong></a>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#d6ebf611cefbf0b1e0d40019e29253fbd1e6e981"><strong>src/busco/GeneSetAnalysis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,17 +24,17 @@ class GeneSetAnalysis(ProteinAnalysis, BuscoAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'proteins'</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">config</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> Initialize an instance.</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> :param params: Values of all parameters that have to be defined</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> :type params: PipeConfig</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">config</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">:</span> <span class="n" style="color: #333;">record</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">))}</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">_</span>cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,11 +42,7 @@ class GeneSetAnalysis(ProteinAnalysis, BuscoAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_buscos_to_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">write_buscos_to_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._tarzip:</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;"># self._run_tarzip_hmmer_output()</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span></pre>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_dirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">create_dirs</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#d1bb5c571aba1a9dd63ad9538318c32ffd274023"><strong>src/busco/GenomeAnalysis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,19 +12,16 @@ Licensed under the MIT license. See LICENSE.md file.</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</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;">busco.BuscoAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoAnalysis</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;">busco.Analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NucleotideAnalysis</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoTools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ProdigalRunner</span><span class="p">,</span> <span class="n" style="color: #333;">AugustusRunner</span><span class="p">,</span> <span class="n" style="color: #333;">GFF2GBRunner</span><span class="p">,</span> <span class="n" style="color: #333;">NewSpeciesRunner</span><span class="p">,</span> <span class="n" style="color: #333;">ETrainingRunner</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">OptimizeAugustusRunner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">NoGenesError</span></span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">busco.BuscoConfig</span></span><span class="idiff"> </span><span class="kn" style="font-weight: 600;"><span class="idiff">import</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">BuscoConfigAuto</span></span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoTools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ProdigalRunner</span><span class="p">,</span> <span class="n" style="color: #333;">AugustusRunner</span><span class="p">,</span> <span class="n" style="color: #333;">GFF2GBRunner</span><span class="p">,</span> <span class="n" style="color: #333;">NewSpeciesRunner</span><span class="p">,</span> <span class="n" style="color: #333;">ETrainingRunner</span><span class="p">,</span> <span class="idiff left right">\</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">OptimizeAugustusRunner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">NoGenesError</span></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</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;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoLogger</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">LogDecorator</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">log</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.Toolset</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Tool</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABCMeta</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">configparser</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NoOptionError</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" 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">@@ -32,25 +29,13 @@ class GenomeAnalysis(NucleotideAnalysis, BuscoAnalysis, metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"genome"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">config</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">config</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_dirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">create_dirs</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_tool_dependencies</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> check dependencies on tools</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if a Tool is not available</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">check_tool_dependencies</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> Initialize tools needed for Genome Analysis.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" 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">@@ -58,7 +43,6 @@ class GenomeAnalysis(NucleotideAnalysis, BuscoAnalysis, metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">init_tools</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def _run_tarzip_augustus_output(self): # Todo: rewrite using tarfile</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;"># """</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function tarzips results folder</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">@@ -87,20 +71,12 @@ class GenomeAnalysis(NucleotideAnalysis, BuscoAnalysis, metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "%ssingle_copy_busco_sequences.tar.gz" % self.main_out,</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "single_copy_busco_sequences", "--remove-files"], "bash", shell=False)</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_rerun_busco_command</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">clargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> This function sets the command line to call to reproduce this run</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">clargs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"-sp"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">set_rerun_busco_command</span><span class="p">(</span><span class="n" style="color: #333;">clargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_write_full_table_header</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> This function adds a header line to the full table file</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> :param out: a full table file</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;"> :type out: file</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Busco id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Status</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Contig</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Start</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">End</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Length</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="LC74" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def set_rerun_busco_command(self, clargs):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function sets the command line to call to reproduce this run</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># clargs.extend(["-sp", self._target_species])</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># super().set_rerun_busco_command(clargs)</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GenomeAnalysisProkaryotes</span><span class="p">(</span><span class="n" style="color: #333;">GenomeAnalysis</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">@@ -108,107 +84,32 @@ class GenomeAnalysisProkaryotes(GenomeAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> This class runs a BUSCO analysis on a genome.</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">config</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> Initialize an instance.</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"><span class="s" style="color: #d14;"> :param config: Values of all parameters that have to be defined</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;"> :type config: PipeConfig</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">load_persistent_tools</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Get genetic_code from dataset.cfg file</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># bacteria/archaea=11; Entomoplasmatales,Mycoplasmatales=4</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_genetic_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"prodigal"</span><span class="p">,</span> <span class="s" style="color: #d14;">"prodigal_genetic_code"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">NoOptionError</span><span class="p">:</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_genetic_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"11"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_genetic_code</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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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_cd_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"prodigal"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ambiguous_cd_range_lower"</span><span class="p">)),</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"prodigal"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ambiguous_cd_range_upper"</span><span class="p">))]</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">NoOptionError</span><span class="p">:</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Dataset config file does not contain required information. Please upgrade datasets."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_cd_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">None</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="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">code_4_selected</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"prodigal_output"</span><span class="p">)</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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139
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># tmp_path = os.path.join(self.prodigal_output_dir, "tmp")</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if os.path.exists(tmp_path):</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># shutil.rmtree(tmp_path)</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">_cleanup</span><span class="p">()</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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145
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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146
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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147
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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148
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> This function calls all needed steps for running the analysis.</span></span>
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149
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Initialize tools and check dependencies</span></span>
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151
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_output_dir</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># If prodigal has already been run on the input, don't run it again</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_output_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_prodigal</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">persistent_tools</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">)</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">genetic_code</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_genetic_code</span><span class="p">):</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">genetic_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_genetic_code</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">cd_lower</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">cd_upper</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_cd_range</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_prodigal</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Prodigal has already been run on input. Don't run again, just load necessary params.</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># First determine which GC to use</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">select_optimal_results</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_genetic_code</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_cd_range</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">tmp_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc_run_results</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc</span><span class="p">][</span><span class="s" style="color: #d14;">"tmp_name"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc_run_results</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc</span><span class="p">][</span><span class="s" style="color: #d14;">"log_file"</span><span class="p">]</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">_organize_prodigal_files</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">code_4_selected</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"4"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="172" 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="LC172" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc_run_results</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc</span><span class="p">][</span><span class="s" style="color: #d14;">"seqs_nt"</span><span class="p">]</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc_run_results</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc</span><span class="p">][</span><span class="s" style="color: #d14;">"seqs_aa"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc_run_results</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gc</span><span class="p">][</span><span class="s" style="color: #d14;">"gene_details"</span><span class="p">]</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_prodigal</span><span class="p">()</span></span>
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175
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_faa</span><span class="p">)</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>write_buscos_to_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">)</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">write_buscos_to_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">)</span></span>
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177
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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178
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">load_persistent_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"><span class="s" style="color: #d14;"> For multiple runs, load Prodigal Runner in the same state as the previous run, to avoid having to run Prodigal</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"><span class="s" style="color: #d14;"> on the input again.</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tool</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">.</span><span class="n" style="color: #333;">persistent_tools</span><span class="p">:</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">tool</span><span class="p">,</span> <span class="n" style="color: #333;">ProdigalRunner</span><span class="p">):</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tool</span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized persistent tool."</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_dirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">create_dirs</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_tool_dependencies</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;"> check dependencies on tools</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if a Tool is not available</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">check_tool_dependencies</span><span class="p">()</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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202
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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203
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> Init the tools needed for the analysis</span></span>
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204
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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205
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">init_tools</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_prodigal_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_prodigal_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"prodigal"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Prodigal should be a tool"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProdigalRunner</span><span class="p">()</span></span>
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212
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>
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213
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"***** Run Prodigal on input to predict and extract genes *****"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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214
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_prodigal</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -216,69 +117,64 @@ class GenomeAnalysisProkaryotes(GenomeAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> Run Prodigal on input file to detect genes.</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"prodigal_runner"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProdigalRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_prodigal_tool</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_output_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_genetic_code</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous_cd_range</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">code_4_selected</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">code_4_selected</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping Prodigal run as it has already completed"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">get_gene_details</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC123" 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="LC124" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">prodigal_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_write_full_table_header</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"><span class="s" style="color: #d14;"> This function adds a header line to the full table file</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"><span class="s" style="color: #d14;"> :param out: a full table file</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"><span class="s" style="color: #d14;"> :type out: file</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Busco id</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Status</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Contig</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Start</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">End</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Length</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="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GenomeAnalysisEukaryotes</span><span class="p">(</span><span class="n" style="color: #333;">GenomeAnalysis</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"><span class="s" style="color: #d14;"> This class runs a BUSCO analysis on a euk_genome.</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"><span class="s" style="color: #d14;"> Todo: reintroduce restart mode with checkpoints</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="s" style="color: #d14;"> This class runs a BUSCO analysis on a eukaryote genome.</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> Retrieve the augustus config path, mandatory for genome</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;"> Cannot be specified through config because some augustus perl scripts use it as well</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"><span class="s" style="color: #d14;"> BUSCO could export it if absent, but do not want to mess up with the user env,</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"><span class="s" style="color: #d14;"> let's just tell the user to do it for now.</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;"> :param config: Values of all parameters that have to be defined</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"><span class="s" style="color: #d14;"> :type config: PipeConfig</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_config_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">environ</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"AUGUSTUS_CONFIG_PATH"</span><span class="p">)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"long"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC142" 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="LC252" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_species"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_species"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Something went wrong. Eukaryota datasets should specify an augustus species."</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_parameters"</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">,</span> <span class="s" style="color: #d14;">' '</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_parameters"</span><span class="p">).</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">,</span> <span class="s" style="color: #d14;">' '</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">NoOptionError</span><span class="p">:</span></span>
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258
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_parameters</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="LC259" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_file_dependencies</span><span class="p">()</span></span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mkblast_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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263
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gff2gb_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">etraining_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_augustus_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"></span>
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264
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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265
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_dirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">create_dirs</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_tool_dependencies</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">blast_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_blast_version</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">blast_version</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"2.2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2.3"</span><span class="p">]:</span> <span class="c1" style="color: #998; font-style: italic;"># Known problems with multithreading on BLAST 2.4-2.9.</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">blast_version</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"2.9"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="s" style="color: #d14;">"tblastn_June13"</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># NCBI sent a binary with this name that avoids the multithreading problems.</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC276" 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="LC277" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"You are using BLAST version {}. This is known to yield inconsistent results when "</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="s" style="color: #d14;">"multithreading. BLAST will run on a single core as a result. For performance improvement, "</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="s" style="color: #d14;">"please revert to BLAST 2.2 or 2.3."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">blast_version</span><span class="p">))</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blast_cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">check_tool_dependencies</span><span class="p">()</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> This function cleans temporary files</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">augustus_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span> <span class="c1" style="color: #998; font-style: italic;"># Should be already done if AugustusRunner ran correctly</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">augustus_tmp</span><span class="p">):</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">augustus_tmp</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"BUSCO"</span><span class="p">):</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">move_retraining_parameters</span><span class="p">()</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">:</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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282
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"></span>
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283
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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284
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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">@@ -287,289 +183,131 @@ class GenomeAnalysisEukaryotes(GenomeAnalysis):</td>
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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288
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">init_tools</span><span class="p">()</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mkblast_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mkblast_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"makeblastdb"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"mkblast should be a tool"</span><span class="p">)</span></span>
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296
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"tblastn"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"tblastn should be a tool"</span><span class="p">)</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"augustus"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">,</span> <span class="n" style="color: #333;">augustus_out</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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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For some reason Augustus appears to send a return code before it writes to stdout, so we have to</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sleep briefly to allow the output to be written to the file. Otherwise we have a truncated output which</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># will cause an error.</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._augustus_tool.sleep = 0.4</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Augustus should be a tool"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff2gbSmallDNA_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff2gbSmallDNA_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"gff2gbSmallDNA.pl"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"gff2gbSmallDNA.pl should be a tool"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_new_species_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_new_species_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"new_species.pl"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"new_species.pl should be a tool"</span><span class="p">)</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_etraining_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_etraining_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"etraining"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"etraining should be a tool"</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AugustusRunner</span><span class="p">()</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gff2gb_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GFF2GBRunner</span><span class="p">()</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NewSpeciesRunner</span><span class="p">()</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">etraining_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ETrainingRunner</span><span class="p">()</span></span>
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>
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335
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_long</span><span class="p">:</span></span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_optimize_augustus_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_optimize_augustus_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize_augustus.pl"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"optimize_augustus should be a tool"</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_augustus_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptimizeAugustusRunner</span><span class="p">()</span></span>
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342
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>
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343
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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344
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"></span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Running Augustus gene predictor on BLAST search results."</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_augustus</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">rerun</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="LC347" class="line" lang="python"> <span class="n" style="color: #333;">output_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_output"</span><span class="p">)</span></span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># TODO: consider grouping all create_dir calls into one function for all tools</span></span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">)</span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self.augustus_runner:</span></span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.augustus_runner.coords = coords</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.augustus_runner.target_species = self._target_species</span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># else:</span></span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AugustusRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_tool</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_seqs</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">,</span></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lineage_dataset</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_parameters</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span><span class="p">,</span></span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_folder</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">,</span> <span class="n" style="color: #333;">rerun</span><span class="p">)</span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span></span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="s" style="color: #d14;">"""This function calls all needed steps for running the analysis."""</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_mkblast</span><span class="p">()</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_tblastn</span><span class="p">()</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_augustus</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_sequences</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_rerun_augustus</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_tool</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># Reset job count</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_tool</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</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="LC208" class="line" lang="python"> <span class="n" style="color: #333;">missing_and_fragmented_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">missing_buscos</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span></span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">fragmented_buscos</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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366
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Re-running Augustus with the new metaparameters, number of target BUSCOs: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_and_fragmented_buscos</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">missing_and_fragmented_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">busco</span><span class="p">:</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">busco</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">busco</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">coords</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">missing_and_fragmented_buscos</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">missing_and_fragmented_coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">busco</span><span class="p">:</span> <span class="n" style="color: #333;">coords</span><span class="p">[</span><span class="n" style="color: #333;">busco</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">busco</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">coords</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">busco</span> <span class="ow" style="font-weight: 600;">in</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">missing_and_fragmented_buscos</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'Trained species folder is {}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_augustus</span><span class="p">(</span><span class="n" style="color: #333;">missing_and_fragmented_coords</span><span class="p">,</span> <span class="n" style="color: #333;">rerun</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="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_set_checkpoint</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"><span class="s" style="color: #d14;"> This function update the checkpoint file with the provided id or delete</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"><span class="s" style="color: #d14;"> it if none is provided</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;"> :param id: the id of the checkpoint</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"><span class="s" style="color: #d14;"> :type id: int</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">checkpoint_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"checkpoint.tmp"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">id</span><span class="p">:</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">checkpoint_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">checkpt_file</span><span class="p">:</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">checkpt_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"{}.{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mode</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC384" 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="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">checkpoint_filename</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">checkpoint_filename</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_gff2gb</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gff2gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GFF2GBRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gff2gbSmallDNA_tool</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_input_file</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">single_copy_buscos</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gff2gb</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_new_species</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">new_species_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BUSCO_{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NewSpeciesRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_new_species_tool</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_domain</span><span class="p">,</span> <span class="n" style="color: #333;">new_species_name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># create new species config file from template</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">new_species_name</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_etraining</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># train on new training set (complete single copy buscos)</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">etraining_runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ETrainingRunner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_etraining_tool</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_folder</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_cpus</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_config_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">etraining_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"><span class="s" style="color: #d14;"> This function calls all needed steps for running the analysis.</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"><span class="s" style="color: #d14;"> Todo: reintroduce checkpoints and restart option.</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_mkblast</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_tblastn</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_augustus</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gene_details</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_sequences</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rerun_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Starting second step of analysis. The gene predictor Augustus is retrained using the results from the "</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"> <span class="s" style="color: #d14;">"initial run to yield more accurate results."</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rerun_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"></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;"># self._fix_restart_augustus_folder() # todo: reintegrate this when checkpoints are restored</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">coords</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_tblastn</span><span class="p">(</span><span class="n" style="color: #333;">missing_and_frag_only</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">ancestral_variants</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_has_variants_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Training Augustus using Single-Copy Complete BUSCOs:"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Converting predicted genes to short genbank files"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_rerun_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">make_gff_files</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">single_copy_buscos</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_tblastn</span><span class="p">(</span><span class="n" style="color: #333;">missing_and_frag_only</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">ancestral_variants</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_has_variants_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_gff2gb</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"All files converted to short genbank files, now running the training scripts"</span><span class="p">)</span></span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"> <span class="n" style="color: #333;">new_species_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_new_species</span><span class="p">()</span></span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_species_name</span> <span class="c1" style="color: #998; font-style: italic;"># todo: check new species folder can be read/written - detect any silent Augustus issues</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_merge_gb_files</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_new_species</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_species"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span><span class="p">.</span><span class="n" style="color: #333;">new_species_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span><span class="p">.</span><span class="n" style="color: #333;">new_species_name</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_etraining</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_long</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_optimize_augustus</span><span class="p">(</span><span class="n" style="color: #333;">new_species_name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_optimize_augustus</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">new_species_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">new_species_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_etraining</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC234" 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="LC447" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_augustus</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>gene_details</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_rerun_augustus</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tblastn_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">gene_details</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_sequences</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>write_buscos_to_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">hmmer_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">write_buscos_to_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">NoGenesError</span><span class="p">:</span></span>
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452
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"No genes found on Augustus rerun."</span><span class="p">)</span></span>
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453
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._move_retraining_parameters()</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._tarzip:</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._tarzip: # todo: zip folders with a lot of output</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._run_tarzip_augustus_output()</span></span>
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457
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._run_tarzip_hmmer_output()</span></span>
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458
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># remove the checkpoint, run is done</span></span>
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459
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._set_checkpoint()</span></span>
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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461
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_file_dependencies</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: currently only implemented for GenomeAnalysisEukaryotes, checking Augustus dirs. Does it need to be rolled out for all analyses?</span></span>
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463
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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464
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"><span class="s" style="color: #d14;"> check dependencies on files and folders</span></span>
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465
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"><span class="s" style="color: #d14;"> properly configured.</span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if Augustus config path is not writable or</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"><span class="s" style="color: #d14;"> not set at all</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if Augustus config path does not contain</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"><span class="s" style="color: #d14;"> the needed species</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"><span class="s" style="color: #d14;"> present</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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473
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">augustus_species_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_config_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"species"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span><span class="n" style="color: #333;">augustus_species_dir</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">W_OK</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot write to Augustus species folder, please make sure you have write "</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="s" style="color: #d14;">"permissions to {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">augustus_species_dir</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="python"> <span class="s" style="color: #d14;">"The environment variable AUGUSTUS_CONFIG_PATH is not set"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">augustus_species_dir</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="python"> <span class="s" style="color: #d14;">"Impossible to locate the species </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">{0}</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> in Augustus species folder"</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="s" style="color: #d14;">" ({1}), check that AUGUSTUS_CONFIG_PATH is properly set"</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> <span class="s" style="color: #d14;">" and contains this species. </span><span class="se" style="color: #d14;">\n\t\t</span><span class="s" style="color: #d14;">See the help if you want "</span></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"> <span class="s" style="color: #d14;">"to provide an alternative species"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">,</span> <span class="n" style="color: #333;">augustus_species_dir</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_rerun_busco_command</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">clargs</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"><span class="s" style="color: #d14;"> This function sets the command line to call to reproduce this run</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">clargs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"-sp"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_parameters</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">clargs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">"--augustus_parameters"</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;">%s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_parameters</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">set_rerun_busco_command</span><span class="p">(</span><span class="n" style="color: #333;">clargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"></span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"><span class="s" style="color: #d14;"> This function cleans temporary files</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">augustus_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">tmp_dir</span> <span class="c1" style="color: #998; font-style: italic;"># Should be already done if AugustusRunner ran correctly</span></span>
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">augustus_tmp</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">augustus_tmp</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"BUSCO"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_move_retraining_parameters</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">_cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_fix_restart_augustus_folder</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"><span class="s" style="color: #d14;"> This function resets and checks the augustus folder to make a restart</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"><span class="s" style="color: #d14;"> possible in phase 2</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="python"><span class="s" style="color: #d14;"> :raises SystemExit: if it is not possible to fix the folders</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"><span class="s" style="color: #d14;"> # Todo: reintegrate this when restart option is added back</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"predicted_genes_run1"</span><span class="p">))</span> \</span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmmer_output_run1"</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"predicted_genes"</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="LC527" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"predicted_genes"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"predicted_genes_run1"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"predicted_genes"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmmer_output"</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="LC533" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rmdir</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmmer_output"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmmer_output_run1"</span><span class="p">),</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmmer_output"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Running Augustus gene predictor on BLAST search results."</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_augustus</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="n" style="color: #333;">rerun</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="LC251" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">configure_runner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">coords</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span><span class="p">,</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span><span class="p">,</span> <span class="n" style="color: #333;">rerun</span><span class="p">)</span></span>
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536
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">run</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2nd"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rerun</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"1st"</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping {} augustus run as output already processed"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">))</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">process_output</span><span class="p">()</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_nt</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">sequences_aa</span></span>
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537
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"augustus_output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"predicted_genes"</span><span class="p">))</span></span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"hmmer_output"</span><span class="p">))):</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_etraining</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="s" style="color: #d14;">"""Train on new training set (complete single copy buscos)"""</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">etraining_runner</span><span class="p">.</span><span class="n" style="color: #333;">configure_runner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span><span class="p">.</span><span class="n" style="color: #333;">new_species_name</span><span class="p">)</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">etraining_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping etraining as it has already been done"</span><span class="p">)</span></span>
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541
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Impossible to restart the run, necessary folders are missing. Use the -f option instead of -r"</span><span class="p">)</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">etraining_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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544
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_move_retraining_parameters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="python"><span class="s" style="color: #d14;"> This function moves retraining parameters from augustus species folder</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"><span class="s" style="color: #d14;"> to the run folder</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">augustus_species_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_augustus_config_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"species"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">augustus_species_path</span><span class="p">):</span></span>
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552
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="n" style="color: #333;">new_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"retraining_parameters"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_target_species</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">augustus_species_path</span><span class="p">,</span> <span class="n" style="color: #333;">new_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Converting predicted genes to short genbank files"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_gff2gb</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gff2gb_runner</span><span class="p">.</span><span class="n" style="color: #333;">configure_runner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">single_copy_buscos</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gff2gb_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping gff2gb conversion as it has already been done"</span><span class="p">)</span></span>
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554
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Augustus did not produce a retrained species folder."</span><span class="p">)</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gff2gb_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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556
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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557
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_merge_gb_files</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"concat all gb files..."</span><span class="p">)</span></span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Concatenate all GB files into one large file</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"training_set.db"</span><span class="p">),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outfile</span><span class="p">:</span></span>
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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="python"> <span class="n" style="color: #333;">gb_dir_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"gb"</span><span class="p">)</span></span>
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563
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">gb_dir_path</span><span class="p">):</span></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">gb_dir_path</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">),</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">infile</span><span class="p">:</span></span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">writelines</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">())</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_new_species</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="s" style="color: #d14;">"""Create new species config file from template"""</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span><span class="p">.</span><span class="n" style="color: #333;">check_previous_completed_run</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Skipping new species creation as it has already been done"</span><span class="p">)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"restart"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">restart</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">new_species_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_optimize_augustus</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">new_species_name</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># long mode (--long) option - runs all the Augustus optimization</span></span>
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># scripts (adds ~1 day of runtime)</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="s" style="color: #d14;">""" long mode (--long) option - runs all the Augustus optimization scripts (adds ~1 day of runtime)"""</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Optimizing augustus metaparameters, this may take a very long time, started at {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%m/%d/%Y %H:%M:%S"</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_augustus_runner</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">OptimizeAugustusRunner</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_optimize_augustus_tool</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">augustus_runner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">output_folder</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">new_species_name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_cpus</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_augustus_runner</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">configure_runner</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">augustus_runner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">output_folder</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">new_species_name</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">optimize_augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def set_rerun_busco_command(self, clargs):</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function sets the command line to call to reproduce this run</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># clargs.extend(["-sp", self._target_species])</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._augustus_parameters:</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># clargs.extend(["--augustus_parameters", "\"%s\"" % self._augustus_parameters])</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># super().set_rerun_busco_command(clargs)</span></span></pre>
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<li id="a6fed85d58ca22cbfd88df357244e6f9fc6faa70">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#a6fed85d58ca22cbfd88df357244e6f9fc6faa70"><strong>src/busco/Toolset.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +13,12 @@ Licensed under the MIT license. See LICENSE.md file.</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">threading</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">subprocess</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TimeoutExpired</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># import threading</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Process</span><span class="p">,</span> <span class="n" style="color: #333;">Pool</span><span class="p">,</span> <span class="n" style="color: #333;">Value</span><span class="p">,</span> <span class="n" style="color: #333;">Lock</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">shutil</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">which</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABCMeta</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">,</span> <span class="n" style="color: #333;">ToolLogger</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">LogDecorator</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">log</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StreamLogger</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">@@ -23,12 +26,12 @@ import logging</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Job</span><span class="p">(</span><span class="n" style="color: #333;">threading</span><span class="p">.</span><span class="n" style="color: #333;">Thread</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Job</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">Process</span></span><span class="p"><span class="idiff">):</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#</span>threading.Thread):</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> Build and executes one work item in an external process</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tool_name</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">job_outlogger</span><span class="p">,</span> <span class="n" style="color: #333;">job_errlogger</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tool_name</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">job_outlogger</span><span class="p">,</span> <span class="n" style="color: #333;">job_errlogger</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">timeout</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> :param name: a name of an executable / script ("a tool") to be run</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> :type cmd: list</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">@@ -42,6 +45,7 @@ class Job(threading.Thread):</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">cmd</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_outlogger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">job_outlogger</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_errlogger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">job_errlogger</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">timeout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">timeout</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_parameter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">parameter</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">@@ -60,14 +64,22 @@ class Job(threading.Thread):</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">StreamLogger</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_outlogger</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">out</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># kwargs only provided to out to capture augustus stdout</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">StreamLogger</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">ERROR</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_errlogger</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">err</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Stick with Popen(), communicate() and wait() instead of just run() to ensure compatibility with</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Python versions < 3.5.</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd_line</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;">False</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">err</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">wait</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Stick with Popen(), communicate() and wait() instead of just run() to ensure compatibility with</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Python versions < 3.5.</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd_line</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;">False</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">err</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">wait</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">timeout</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">TimeoutExpired</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">kill</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"The following job was killed as it was taking too long (>1hr) to "</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="s" style="color: #d14;">"complete.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd_line</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_outlogger</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_outlogger</span><span class="p">.</span><span class="n" style="color: #333;">removeHandler</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_outlogger</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_errlogger</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_errlogger</span><span class="p">.</span><span class="n" style="color: #333;">removeHandler</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">job_errlogger</span><span class="p">.</span><span class="n" style="color: #333;">_file_hdlr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">cnt</span><span class="p">.</span><span class="n" style="color: #333;">get_lock</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span><span class="p">.</span><span class="n" style="color: #333;">value</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="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ToolException</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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">@@ -80,12 +92,12 @@ class ToolException(Exception):</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Tool</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Tool</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">metaclass</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">ABCMeta</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> Collection of utility methods used by all tools</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff right">kwargs</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> Initialize job list for a tool</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> :param name: the name of the tool to execute</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,51 +106,45 @@ class Tool:</td>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> :type config: configparser.ConfigParser</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_tool_available</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ToolException</span><span class="p">(</span><span class="s" style="color: #d14;">"{} tool cannot be found. Please check the 'path' and 'command' parameters "</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">"provided in the config file. Do not include the command in the path!"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logfile_path_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_set_logfile_path</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logfile_path_err</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logfile_path_out</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_out.log'</span><span class="p">,</span> <span class="s" style="color: #d14;">'_err.log'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.name = name</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if not self.check_tool_available():</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># raise ToolException("{} tool cannot be found. Please check the 'path' and 'command' parameters "</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># "provided in the config file. Do not include the command in the path!".format(self.name))</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</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;">"augustus"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"augustus_out"</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">timeout</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3600</span></span>
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<pre style="margin: 0;">+<span id="LC117" 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="LC118" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">timeout</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_to_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_running</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</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="LC123" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">count_jobs_created</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logged_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">chunksize</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.count_jobs_created = True</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.logged_header = False</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_tool_available</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> Check tool's availability.</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> 1. The section ['name'] is available in the config</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;"> 2. This section contains keys 'path' and 'command'</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> 3. The string resulted from contatination of values of these two keys</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> represents the full path to the command</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> :param name: the name of the tool to execute</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;"> :type name: str</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> :param config: initialized instance of ConfigParser</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;"> :type config: configparser.ConfigParser</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> :return: True if the tool can be run, False if it is not the case</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> :rtype: bool</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">has_section</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ToolException</span><span class="p">(</span><span class="s" style="color: #d14;">"Section for the tool [{}] is not present in the config file"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.logfile_path_out = os.path.join(self.config.get("busco_run", "main_out"), "logs", "{}_out.log".format(self.name))</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.logfile_path_err = self.logfile_path_out.replace('_out.log', '_err.log')</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">has_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'path'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">ToolException</span><span class="p">(</span><span class="s" style="color: #d14;">"Key </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">path</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> in the section [{}] is not present in the config file"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">configure_job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">has_option</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'command'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">executable</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'command'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC136" 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="LC137" class="line" lang="python"> <span class="n" style="color: #333;">executable</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_job_args</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">'path'</span><span class="p">),</span> <span class="n" style="color: #333;">executable</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">which</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">)</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="c1" style="color: #998; font-style: italic;"># True if tool available</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write_checkpoint_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,10 +152,10 @@ class Tool:</td>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tool_outlogger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ToolLogger</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logfile_path_out</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tool_errlogger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ToolLogger</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logfile_path_err</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">job</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">[:],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tool_outlogger</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tool_errlogger</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">job</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">[:],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tool_outlogger</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tool_errlogger</span><span class="p">,</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">timeout</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">**</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_to_run</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">count_jobs_created</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>if self.count_jobs_created:</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># </span> self.total += 1</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">job</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">job</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">@@ -160,45 +166,44 @@ class Tool:</td>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_to_run</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">job</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_set_logfile_path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">),</span> <span class="s" style="color: #d14;">"logs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}_out.log"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"Running {} job(s) on {}"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'total'</span><span class="p">,</span> <span class="s" style="color: #d14;">'name'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">log_jobs_to_run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logged_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Running {} job(s) on {}, starting at {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">'%m/%d/%Y %H:%M:%S'</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_jobs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">max_threads</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;"> This method run all jobs created for the Tool and redirect</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"><span class="s" style="color: #d14;"> the standard output and error to the current logger</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"><span class="s" style="color: #d14;"> :param max_threads: the number or threads to run simultaneously</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"><span class="s" style="color: #d14;"> :type max_threads: int</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"><span class="s" style="color: #d14;"> :param log_it: whether to log the progress for the tasks. Default True</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"><span class="s" style="color: #d14;"> :type log_it: boolean</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logged_header</span><span class="p">:</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">"No jobs to run on {}"</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="n" style="color: #333;">iswarn</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="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">log_no_jobs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_jobs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_jobs_to_run</span><span class="p">()</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">log_no_jobs</span><span class="p">()</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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181
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Wait for all threads to finish and log progress</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">already_logged</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_to_run</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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_running</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">sleep</span><span class="p">(</span><span class="mf" style="color: #099;">0.001</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_to_run</span><span class="p">:</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_running</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_threads</span><span class="p">:</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_running</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_to_run</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">j</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">()</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_running</span><span class="p">:</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># j.join()</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">j</span><span class="p">.</span><span class="n" style="color: #333;">is_alive</span><span class="p">():</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">jobs_running</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">10</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="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">already_logged</span><span class="p">:</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">already_logged</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_track_progress</span><span class="p">()</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.total = 0 # Reset for tools that are run twice (tblastn, augustus)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cpus</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># todo: need a different way to ensure self.cpus is nonzero number.</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Number of CPUs not specified."</span><span class="p">)</span></span>
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200
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Pool</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">cpus</span><span class="p">,</span> <span class="n" style="color: #333;">initializer</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">).</span><span class="n" style="color: #333;">init_globals</span><span class="p">,</span> <span class="n" style="color: #333;">initargs</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">Value</span><span class="p">(</span><span class="s" style="color: #d14;">'i'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">),))</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">job_pool</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">job_pool</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_job</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">generate_job_args</span><span class="p">(),</span> <span class="n" style="color: #333;">chunksize</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">chunksize</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">write_checkpoint_file</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_job</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,))</span> <span class="c1" style="color: #998; font-style: italic;"># Ensure args are tuples that can be unpacked. If no args, args=None, which is falsy, and this evaluates to (None,)</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">job</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">configure_job</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">job</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">()</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnt</span><span class="p">.</span><span class="n" style="color: #333;">value</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</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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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_track_progress</span><span class="p">()</span></span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'[{0}]</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{1} of {2} task(s) completed'</span><span class="p">,</span> <span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">attr_name</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'nb_done'</span><span class="p">,</span> <span class="s" style="color: #d14;">'total'</span><span class="p">],</span> <span class="n" style="color: #333;">on_func_exit</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="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_track_progress</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">nb_done</span></span></pre>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_globals</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">counter</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">"""Counter code adapted from the answer here: https://stackoverflow.com/a/53621343/4844311"""</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">cnt</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counter</span></span></pre>
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<li id="a2bbc032e6ed94eee5944cfbd98d5754a5fed726">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#a2bbc032e6ed94eee5944cfbd98d5754a5fed726"><strong>src/busco/TranscriptomeAnalysis.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,8 +11,6 @@ Licensed under the MIT license. See LICENSE.md file.</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</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="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoAnalysis</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoLogger</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">LogDecorator</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">log</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">@@ -20,13 +18,13 @@ from Bio.Seq import reverse_complement, translate</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.SeqRecord</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqRecord</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.Analysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NucleotideAnalysis</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">busco.Toolset</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Tool</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># todo: catch multiple buscos on one transcript</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TranscriptomeAnalysis</span><span class="p">(</span><span class="n" style="color: #333;">NucleotideAnalysis</span><span class="p">,</span> <span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> Analysis on a transcriptome.</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">@@ -34,14 +32,11 @@ class TranscriptomeAnalysis(NucleotideAnalysis, BuscoAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"transcriptome"</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">config</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> Initialize an instance.</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> :param config: Values of all parameters that have to be defined</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> :type config: BuscoConfig</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,57 +53,29 @@ class TranscriptomeAnalysis(NucleotideAnalysis, BuscoAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if checkpoint < 1:</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_mkblast</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">coords</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_tblastn</span><span class="p">(</span><span class="n" style="color: #333;">ancestral_variants</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_has_variants_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_tblastn</span><span class="p">(</span><span class="n" style="color: #333;">ancestral_variants</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_has_variants_file</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">protein_seq_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_translate_seqs</span><span class="p">(</span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">protein_seq_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_translate_seqs</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tblastn_runner</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">coords</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_hmmer</span><span class="p">(</span><span class="n" style="color: #333;">protein_seq_files</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Note BUSCO matches are not written to file, as we have not yet developed a suitable protocol for<span class="idiff left right"> Transcriptomes</span></span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_cleanup</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Note BUSCO matches are not written to file, as we have not yet developed a suitable protocol for</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># Transcriptomes</span></span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._tarzip:</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._run_tarzip_hmmer_output()</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self._run_tarzip_translated_proteins()</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_dirs</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: remove this as abstract method, review all abstract methods</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">create_dirs</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># todo: This should be an abstract method</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">init_tools</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mkblast_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_mkblast_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"makeblastdb"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"mkblast should be a tool"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span><span class="p">,</span> <span class="n" style="color: #333;">Tool</span><span class="p">))</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tool</span><span class="p">(</span><span class="s" style="color: #d14;">"tblastn"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_config</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AssertionError</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"tblastn should be a tool"</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_tool_dependencies</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">blast_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_blast_version</span><span class="p">()</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">blast_version</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"2.2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2.3"</span><span class="p">]:</span> <span class="c1" style="color: #998; font-style: italic;"># Known problems with multithreading on BLAST 2.4-2.9.</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">blast_version</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"2.9"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tblastn_tool</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="s" style="color: #d14;">"tblastn_June13"</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># NCBI sent a binary with this name that avoids the multithreading problems.</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC99" 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="LC100" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"You are using BLAST version {}. This is known to yield inconsistent results when "</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="s" style="color: #d14;">"multithreading. BLAST will run on a single core as a result. For performance improvement, "</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">"please revert to BLAST 2.2 or 2.3."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">blast_version</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">blast_cpus</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="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cleanup</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> This function cleans temporary files.</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">cleanup</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">six_frame_translation</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">six_frame_translation</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> Gets the sixframe translation for the provided sequence</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"><span class="s" style="color: #d14;"> :param seq: the sequence to be translated</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" 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">@@ -132,7 +99,8 @@ class TranscriptomeAnalysis(NucleotideAnalysis, BuscoAnalysis):</td>
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132
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">translated_seqs</span><span class="p">[</span><span class="n" style="color: #333;">descriptions</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="n" style="color: #333;">anti</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fragment_length</span><span class="p">],</span> <span class="n" style="color: #333;">stop_symbol</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"X"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">translated_seqs</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_reformats_seq_id</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seq_id</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_reformats_seq_id</span><span class="p">(</span><span class="n" style="color: #333;">seq_id</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> This function reformats the sequence id to its original values</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> :param seq_id: the seq id to reformats</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">@@ -160,8 +128,10 @@ class TranscriptomeAnalysis(NucleotideAnalysis, BuscoAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">protein_seq_files</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">output_filename</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">translated_records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contig_info</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">tmp_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_seqs</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.temp"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">contig_name</span><span class="p">[:</span><span class="mi" style="color: #099;">100</span><span class="p">]))</span> <span class="c1" style="color: #998; font-style: italic;"># Avoid very long filenames</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">tmp_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># These files will only ever have one sequence, but BioPython examples always parse them in an iterator.</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">tmp_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">tblastn_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_seqs</span><span class="p">,</span> <span class="s" style="color: #d14;">"{}.temp"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">contig_name</span><span class="p">[:</span><span class="mi" style="color: #099;">100</span><span class="p">]))</span> <span class="c1" style="color: #998; font-style: italic;"># Avoid very long filenames</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">tmp_filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># These files will only ever have one sequence,</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># but BioPython examples always parse them in an iterator.</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">translated_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">six_frame_translation</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">desc_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">translated_seqs</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># There are six possible translated sequences</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">prot_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">translated_seqs</span><span class="p">[</span><span class="n" style="color: #333;">desc_id</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">@@ -172,7 +142,6 @@ class TranscriptomeAnalysis(NucleotideAnalysis, BuscoAnalysis):</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">protein_seq_files</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># def _run_tarzip_translated_proteins(self):</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># """</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function tarzips results folder</span></span>
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<li id="b183fcee25a51af18c90f143ded1ffead1019f47">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#b183fcee25a51af18c90f143ded1ffead1019f47"><strong>src/busco/ViralAnalysis.py</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># coding: utf-8</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">.. module:: ViralAnalysis</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;"> :synopsis: ViralAnalysis implements genome analysis specifics</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">.. versionadded:: 3.0.0</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">.. versionchanged:: 3.0.0</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="s" style="color: #d14;">Copyright (c) 2016-2020, Evgeny Zdobnov (ez@ezlab.org)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">"""</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;">busco.BuscoAnalysis</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoAnalysis</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;">busco.BuscoLogger</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BuscoLogger</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="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoLogger</span><span class="p">.</span><span class="n" style="color: #333;">get_logger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ViralAnalysis</span><span class="p">(</span><span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> This class runs a BUSCO analysis on a gene set.</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"proteins"</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> Initialize an instance.</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> :param params: Values of all parameters that have to be defined</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> :type params: PipeConfig</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># data integrity checks not done by the parent class</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">check_protein_file</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">ViralAnalysis</span><span class="p">.</span><span class="n" style="color: #333;">_logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Please provide a genome file as input or run BUSCO in protein mode (--mode proteins)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_analysis</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> This function calls all needed steps for running the analysis.</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_translate_virus</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">translated_proteins</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_run_hmmer</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if self._tarzip:</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;"># self._run_tarzip_hmmer_output()</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;">_init_tools</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="s" style="color: #d14;"> Init the tools needed for the analysis</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">_init_tools</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run_hmmer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> This function runs hmmsearch.</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">_run_hmmer</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_sixpack</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> Gets the sixframe translation for the provided sequence</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> :param seq: the sequence to be translated</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"><span class="s" style="color: #d14;"> :type seq: str</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"><span class="s" style="color: #d14;"> :return: the six translated sequences</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> :rtype: list</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</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="LC71" class="line" lang="python"> <span class="n" style="color: #333;">s3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:]</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">rev</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="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">letter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq</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="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">.</span><span class="n" style="color: #333;">COMP</span><span class="p">[</span><span class="n" style="color: #333;">letter</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">rev</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">.</span><span class="n" style="color: #333;">COMP</span><span class="p">[</span><span class="s" style="color: #d14;">"N"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rev</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">r2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rev</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="LC80" class="line" lang="python"> <span class="n" style="color: #333;">r3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rev</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:]</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">transc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">frames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">,</span> <span class="n" style="color: #333;">s3</span><span class="p">,</span> <span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r3</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sequence</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">frames</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">part</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="LC85" class="line" lang="python"> <span class="n" style="color: #333;">new</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="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">letter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sequence</span><span class="p">:</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="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;">part</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">new</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">.</span><span class="n" style="color: #333;">CODONS</span><span class="p">[</span><span class="n" style="color: #333;">part</span><span class="p">]</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">new</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"X"</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">part</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">part</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">letter</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">part</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">letter</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" 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;">part</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">new</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">BuscoAnalysis</span><span class="p">.</span><span class="n" style="color: #333;">CODONS</span><span class="p">[</span><span class="n" style="color: #333;">part</span><span class="p">]</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">new</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"X"</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">transc</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">new</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">transc</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> </span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_translate_virus</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> Prepares viral genomes for a BUSCO</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;"> protein analysis.</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> 1) Translate any sequences in 6 frames</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;"> 2) Split the sequences on the stops</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"><span class="s" style="color: #d14;"> 3) Remove sequences shorter than 50aa</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="s" style="color: #d14;"> :return: file name </span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"><span class="s" style="color: #d14;"> :rtype: string</span></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC114" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_sequences</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC115" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mainout</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"translated_proteins.faa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">o1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># parse file, retrieve all sequences</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f1</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">header</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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<pre style="margin: 0;">-<span id="LC122" 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="LC123" class="line" lang="python"> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">header</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># feed sequences to 6 frame translator</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># then split on STOP codons</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">ctg_ct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seqid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">seq_6f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_sixpack</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">seqid</span><span class="p">])</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">nb_frame</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="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">frame</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_6f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">valid_ts_ct</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="LC133" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># chop at the stop codons</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">chopped_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"X"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">short_seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chopped_seqs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># must have at least 50 A.A. to be considered further</span></span>
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<pre style="margin: 0;">-<span id="LC137" 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;">short_seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">50</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ctg nb, frame nb, transcript nb</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">o1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">seq_n%s_f%s_t%s</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="p">(</span><span class="n" style="color: #333;">ctg_ct</span><span class="p">,</span> <span class="n" style="color: #333;">nb_frame</span><span class="p">,</span> <span class="n" style="color: #333;">valid_ts_ct</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">o1</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"%s</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;">short_seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">valid_ts_ct</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="LC142" 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="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">nb_frame</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="LC145" class="line" lang="python"> <span class="n" style="color: #333;">ctg_ct</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="LC146" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">translated_proteins</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">main_out</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"translated_proteins.faa"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88"><strong>src/busco/_version.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,4 +6,4 @@ Copyright (c) 2016-2020, Evgeny Zdobnov (ez@ezlab.org)</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">Licensed under the MIT license. See LICENSE.md file.</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"4.<span class="idiff left right">0.6</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"4.<span class="idiff left right">1.2</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#bd0e703ba072ee7447fcc5bd1e634475b3438cf9"><strong>src/busco/run_BUSCO.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +66,8 @@ def _parse_args():</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="s" style="color: #d14;">'--out_path'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'out_path'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'OUTPUT_PATH'</span><span class="p">,</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Optional location for results folder, excluding results folder name. Default is current working directory.'</span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Optional location for results folder, excluding results folder name. '</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="s" style="color: #d14;">'Default is current working directory.'</span><span class="p">)</span></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">'-e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--evalue'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'evalue'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,6 +90,10 @@ def _parse_args():</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Force rewriting of existing files. '</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">'Must be used when output files with the provided name already exist.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--restart'</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;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'restart'</span><span class="p">,</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Continue a run that had already partially completed.'</span><span class="p">)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"></span>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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93
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">'--limit'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'limit'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'REGION_LIMIT'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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94
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'How many candidate regions (contig or transcript) to consider per BUSCO (default: %s)'</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">@@ -117,7 +122,8 @@ def _parse_args():</td>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># action="store_true")</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">'--auto-lineage'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto-lineage'</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;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Run auto-lineage to find optimum lineage path'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">'--auto-lineage'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto-lineage'</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;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Run auto-lineage to find optimum lineage path'</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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123
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'--auto-lineage-prok'</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'auto-lineage-prok'</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;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,7 +150,8 @@ def _parse_args():</td>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-h'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--help'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CleanHelpAction</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;">"Show this help message and exit"</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--list-datasets'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ListLineagesAction</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;">"Print the list of available BUSCO datasets"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--list-datasets'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ListLineagesAction</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Print the list of available BUSCO datasets"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">())</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="167" 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">@@ -160,7 +167,9 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">params</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="LC168" class="line" lang="python"> <span class="n" style="color: #333;">run_BUSCO</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)</span></span>
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162
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'***** Start a BUSCO v{} analysis, current time: {} *****'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">busco</span><span class="p">.</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">'%m/%d/%Y %H:%M:%S'</span><span class="p">)),</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'***** Start a BUSCO v{} analysis, current time: {} *****'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">busco</span><span class="p">.</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">'%m/%d/%Y %H:%M:%S'</span><span class="p">)),</span> <span class="n" style="color: #333;">logger</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_BUSCO</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">):</span></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -173,14 +182,16 @@ def run_BUSCO(params):</td>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"></span>
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174
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">lineage_basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_dataset"</span><span class="p">))</span></span>
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">main_out_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"main_out"</span><span class="p">)</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">lineage_results_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto_lineage"</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_results_dir"</span><span class="p">))</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">lineage_results_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto_lineage"</span><span class="p">,</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lineage_results_dir"</span><span class="p">))</span></span>
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177
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"></span>
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178
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">getboolean</span><span class="p">(</span><span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage"</span><span class="p">):</span></span>
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179
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineage_basename</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">((</span><span class="s" style="color: #d14;">"bacteria"</span><span class="p">,</span> <span class="s" style="color: #d14;">"archaea"</span><span class="p">,</span> <span class="s" style="color: #d14;">"eukaryota"</span><span class="p">)):</span></span>
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180
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">busco_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_manager</span><span class="p">.</span><span class="n" style="color: #333;">runner</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># It is possible that the following lineages were arrived at either by the Prodigal genetic code shortcut or by</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># BuscoPlacer. If the former, the run will have already been completed. If the latter it still needs to be done.</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># It is possible that the following lineages were arrived at either by the Prodigal genetic code shortcut</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># or by BuscoPlacer. If the former, the run will have already been completed. If the latter it still needs</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># to be done.</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">lineage_basename</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">((</span><span class="s" style="color: #d14;">"mollicutes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mycoplasmatales"</span><span class="p">,</span> <span class="s" style="color: #d14;">"entomoplasmatales"</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">lineage_results_folder</span><span class="p">):</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">busco_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_manager</span><span class="p">.</span><span class="n" style="color: #333;">runner</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">@@ -190,13 +201,13 @@ def run_BUSCO(params):</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">busco_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">lineage_results_folder</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">lineage_results_folder</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"busco_run"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lineage_results_dir"</span></span><span class="p"><span class="idiff right">)))</span></span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">busco_run</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">finish</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">time</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">time</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">start_time</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">root_lineage</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">lineage_results_folder</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">main_out_folder</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"busco_run"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lineage_results_dir"</span></span><span class="p"><span class="idiff right">))</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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196
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">busco_run</span><span class="p">.</span><span class="n" style="color: #333;">run_analysis</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">busco_run</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_results_lines</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">final_results</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">busco_run</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">hmmer_r<span class="idiff left">unner</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">hmmer_r</span>esults_lines</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">BuscoRunner</span><span class="p">.</span><span class="n" style="color: #333;">results_datasets</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lineage_basename</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">busco_run</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start_time</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">busco_run</span><span class="p">.</span><span class="n" style="color: #333;">finish</span><span class="p">(</span><span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start_time</span><span class="p">)</span></span>
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200
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"></span>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">ToolException</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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202
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">e</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">@@ -226,7 +237,8 @@ def run_BUSCO(params):</td>
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"></span>
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227
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">BaseException</span><span class="p">:</span></span>
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228
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">exc_type</span><span class="p">,</span> <span class="n" style="color: #333;">exc_value</span><span class="p">,</span> <span class="n" style="color: #333;">exc_traceback</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">exc_info</span><span class="p">()</span></span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">critical</span><span class="p">(</span><span class="s" style="color: #d14;">"Unhandled exception occurred:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">traceback</span><span class="p">.</span><span class="n" style="color: #333;">format_exception</span><span class="p">(</span><span class="n" style="color: #333;">exc_type</span><span class="p">,</span> <span class="n" style="color: #333;">exc_value</span><span class="p">,</span> <span class="n" style="color: #333;">exc_traceback</span><span class="p">))))</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">critical</span><span class="p">(</span><span class="s" style="color: #d14;">"Unhandled exception occurred:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">traceback</span><span class="p">.</span><span class="n" style="color: #333;">format_exception</span><span class="p">(</span><span class="n" style="color: #333;">exc_type</span><span class="p">,</span> <span class="n" style="color: #333;">exc_value</span><span class="p">,</span> <span class="n" style="color: #333;">exc_traceback</span><span class="p">))))</span></span>
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span></span>
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231
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></span>
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232
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"></span>
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<li id="dba59ea4008347497ea58386e70f0fd75cc9a2e4">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#dba59ea4008347497ea58386e70f0fd75cc9a2e4"><strong>test_data/bacteria/expected_log.txt</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">INFO: ***** Start a BUSCO v4.<span class="idiff left right">0.6 analysis, current time: 02/12/2020 16:38:00</span> *****</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">INFO: ***** Start a BUSCO v4.<span class="idiff left right">1.2 analysis, current time: 07/01/2020 18:43:08</span> *****</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">INFO: Configuring BUSCO with /busco/config/config.ini</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">INFO: Mode is genome</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">INFO: Input file is genome.fna</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,12 +14,12 @@ INFO: Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/archaea_od</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">INFO: Decompressing file '/busco_wd/busco_downloads/lineages/archaea_odb10.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2019-01-04)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">INFO: ***** Run Prodigal on input to predict and extract genes *****</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">INFO: Running <span class="idiff left right">p</span>rodigal with genetic code 11 in single mode</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">INFO: Running 1 job(s) on prodigal</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">INFO: Running <span class="idiff left right">P</span>rodigal with genetic code 11 in single mode</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">INFO: Running 1 job(s) on prodigal<span class="idiff left right">, starting at 07/01/2020 18:43:09</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">INFO: [prodigal] 1 of 1 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">INFO: Genetic code 11 selected as optimal</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">INFO: Running 194 job(s) on hmmsearch</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">INFO: Running 194 job(s) on hmmsearch<span class="idiff left right">, starting at 07/01/2020 18:43:10</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">INFO: [hmmsearch] 20 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">INFO: [hmmsearch] 39 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">INFO: [hmmsearch] 59 of 194 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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="38" 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">@@ -38,13 +38,14 @@ INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2019-06-26</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">INFO: ***** Run Prodigal on input to predict and extract genes *****</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">INFO: Genetic code 11 selected as optimal</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">INFO: Running 124 job(s) on hmmsearch</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">INFO: Running 124 job(s) on hmmsearch<span class="idiff left right">, starting at 07/01/2020 18:43:13</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">INFO: [hmmsearch] 13 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">INFO: [hmmsearch] 25 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">INFO: [hmmsearch] 38 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">INFO: [hmmsearch] 50 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">INFO: [hmmsearch] 63 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">INFO: [hmmsearch] 75 of 124 task(s) completed</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">INFO: [hmmsearch] 87 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">INFO: [hmmsearch] 100 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">INFO: [hmmsearch] 112 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">INFO: [hmmsearch] 124 of 124 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" 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="54" 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">@@ -53,15 +54,15 @@ INFO: Results: C:21.0%[S:21.0%,D:0.0%],F:0.8%,M:78.2%,n:124</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">INFO: Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/eukaryota_odb10.2019-11-20.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">INFO: Decompressing file '/busco_wd/busco_downloads/lineages/eukaryota_odb10.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2019-11-20)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">INFO: Running 1 job(s) on makeblastdb, starting at 07/01/2020 18:43:16</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">INFO: Creating BLAST database with input file</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">INFO: Running 1 job(s) on makeblastdb</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">INFO: [makeblastdb] 1 of 1 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">INFO: Running a BLAST search for BUSCOs against created database</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn<span class="idiff left right">, starting at 07/01/2020 18:43:16</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">INFO: [tblastn] 1 of 1 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">INFO: Running Augustus gene predictor on BLAST search results.</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">INFO: Running Augustus prediction using fly as species:</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">INFO: Running 10 job(s) on augustus</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">INFO: Running 10 job(s) on augustus<span class="idiff left right">, starting at 07/01/2020 18:43:18</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">INFO: [augustus] 1 of 10 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">INFO: [augustus] 2 of 10 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">INFO: [augustus] 3 of 10 task(s) completed</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">@@ -74,7 +75,7 @@ INFO: [augustus] 9 of 10 task(s) completed</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">INFO: [augustus] 10 of 10 task(s) completed</span>
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75
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">INFO: Extracting predicted proteins...</span>
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76
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">INFO: Running 4 job(s) on hmmsearch</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">INFO: Running 4 job(s) on hmmsearch<span class="idiff left right">, starting at 07/01/2020 18:43:51</span></span>
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78
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">INFO: [hmmsearch] 1 of 4 task(s) completed</span>
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79
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">INFO: [hmmsearch] 2 of 4 task(s) completed</span>
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80
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">INFO: [hmmsearch] 3 of 4 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="86" 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">@@ -85,17 +86,19 @@ INFO: Results: C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:255</td>
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85
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">INFO: Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.</span>
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86
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">INFO: Extracting missing and fragmented buscos from the file ancestral_variants...</span>
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87
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">INFO: Running a BLAST search for BUSCOs against created database</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn, starting at 07/01/2020 18:43:52</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">INFO: [tblastn] 1 of 1 task(s) completed</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">INFO: Training Augustus using Single-Copy Complete BUSCOs:</span>
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90
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">INFO: Converting predicted genes to short genbank files</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">INFO: All files converted to short genbank files, now running the training scripts</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">INFO: Running 1 job(s) on new_species.pl</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">WARNING: No jobs to run on gff2gbSmallDNA.pl</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">INFO: All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">INFO: Running 1 job(s) on new_species.pl, starting at 07/01/2020 18:44:07</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">INFO: [new_species.pl] 1 of 1 task(s) completed</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">INFO: Running 1 job(s) on etraining</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">INFO: Running 1 job(s) on etraining<span class="idiff left right">, starting at 07/01/2020 18:44:08</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">INFO: [etraining] 1 of 1 task(s) completed</span>
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96
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">INFO: Re-running Augustus with the new metaparameters, number of target BUSCOs: 255</span>
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97
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">INFO: Running Augustus gene predictor on BLAST search results.</span>
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98
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">INFO: Running Augustus prediction using BUSCO_test_bacteria as species:</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">INFO: Running 14 job(s) on augustus, starting at 07/01/2020 18:44:08</span>
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99
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">INFO: [augustus] 2 of 14 task(s) completed</span>
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100
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">INFO: [augustus] 3 of 14 task(s) completed</span>
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101
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">INFO: [augustus] 5 of 14 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" 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="111" 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">@@ -108,12 +111,11 @@ INFO: [augustus] 13 of 14 task(s) completed</td>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext">INFO: [augustus] 14 of 14 task(s) completed</span>
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109
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">INFO: Extracting predicted proteins...</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">INFO: [hmmsearch] 1 of 3 task(s) completed</span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">INFO: [hmmsearch] 2 of 3 task(s) completed</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">INFO: [hmmsearch] 3 of 3 task(s) completed</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">WARNING: No jobs to run on hmmsearch</span>
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114
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">WARNING: BUSCO did not find any match. Make sure to check the log files if this is unexpected.</span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">INFO: Results: C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:255 </span>
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116
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">WARNING: Augustus did not produce a retrained species folder.</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">INFO: bacteria_odb10 selected</span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">INFO: ***** Searching tree for chosen lineage to find best taxonomic match *****</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" 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="134" 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">@@ -132,7 +134,7 @@ INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxi</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">INFO: Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext">INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.bacteria_odb10.2019-12-16.txt.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">INFO: Place the markers on the reference tree...</span>
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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
135
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<td class="diff-line-num new_line old" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">INFO: Running 1 job(s) on sepp</span>
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<td class="diff-line-num new old_line" data-linenumber="136" 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="137" 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">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">INFO: Running 1 job(s) on sepp<span class="idiff left right">, starting at 07/01/2020 18:44:10</span></span>
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136
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<td class="diff-line-num new_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">INFO: [sepp] 1 of 1 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="137" 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">
137
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<td class="diff-line-num new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">INFO: Not enough markers were placed on the tree (11). Root lineage bacteria is kept</span>
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<td class="diff-line-num old_line" data-linenumber="138" 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">
138
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">INFO: </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -148,12 +150,15 @@ INFO:</td>
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148
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> |97 Missing BUSCOs (M) |</span>
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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
149
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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> |124 Total BUSCO groups searched |</span>
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150
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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"> --------------------------------------------------</span>
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<td class="diff-line-num old old_line" data-linenumber="151" 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">
151
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<td class="diff-line-num new_line old" data-linenumber="153" 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="LC151" class="line" lang="plaintext">INFO: BUSCO analysis done with WARNING(s). Total running time: <span class="idiff left right">81</span> seconds</span>
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<td class="diff-line-num new old_line" data-linenumber="152" 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="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">INFO: BUSCO analysis done with WARNING(s). Total running time: <span class="idiff left right">127</span> seconds</span>
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152
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"></span>
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153
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="plaintext">***** Summary of warnings: *****</span>
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<td class="diff-line-num old_line" data-linenumber="154" 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">
154
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<td class="diff-line-num new_line" data-linenumber="156" 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">
156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext">WARNING:busco.ConfigManager Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>
</pre>
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155
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext">WARNING:busco.BuscoTools BUSCO did not find any match. Make sure to check the log files if this is unexpected.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="156" 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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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">WARNING:busco.Toolset No jobs to run on gff2gbSmallDNA.pl</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">WARNING:busco.Toolset No jobs to run on hmmsearch</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="156" 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">
156
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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
160
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext">WARNING:busco.BuscoTools BUSCO did not find any match. Make sure to check the log files if this is unexpected.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="157" 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="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">WARNING:busco.BuscoTools Augustus did not produce a retrained species folder.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
157
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<td class="diff-line-num new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="158" 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">
158
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<td class="diff-line-num new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext">INFO: Results written in /busco_wd/test_bacteria</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
159
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<td class="diff-line-num new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext"></span></pre>
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<br>
</li>
<li id="11a346fb4c4f7cb01e1e5466e6712687c54fe746">
<a href="https://salsa.debian.org/med-team/busco/-/compare/7e9907ffb042987f6086f0e34d62b6dc3ae2cf72...1c4781f6b08bd870d527196d9dae09387c727d0b#11a346fb4c4f7cb01e1e5466e6712687c54fe746"><strong>test_data/eukaryota/expected_log.txt</strong></a>
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<td class="diff-line-num old old_line" data-linenumber="1" 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">
1
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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">INFO: ***** Start a BUSCO v4.<span class="idiff left right">0.6 analysis, current time: 02/12/2020 16:40:52</span> *****</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" 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="1" 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">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">INFO: ***** Start a BUSCO v4.<span class="idiff left right">1.2 analysis, current time: 07/01/2020 17:20:41</span> *****</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" 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">
2
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<td class="diff-line-num new_line" data-linenumber="2" 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">
2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">INFO: Configuring BUSCO with /busco/config/config.ini</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">INFO: Mode is genome</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">INFO: Input file is genome.fna</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,12 +14,12 @@ INFO: Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/archaea_od</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">INFO: Decompressing file '/busco_wd/busco_downloads/lineages/archaea_odb10.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">INFO: Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2019-01-04)</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">INFO: ***** Run Prodigal on input to predict and extract genes *****</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">INFO: Running <span class="idiff left right">p</span>rodigal with genetic code 11 in single mode</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">INFO: Running 1 job(s) on prodigal</span>
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<td class="diff-line-num new old_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">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">INFO: Running <span class="idiff left right">P</span>rodigal with genetic code 11 in single mode</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">INFO: Running 1 job(s) on prodigal<span class="idiff left right">, starting at 07/01/2020 17:20:42</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">INFO: [prodigal] 1 of 1 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">INFO: Genetic code 11 selected as optimal</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">INFO: Running 194 job(s) on hmmsearch</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">INFO: Running 194 job(s) on hmmsearch<span class="idiff left right">, starting at 07/01/2020 17:20:42</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">INFO: [hmmsearch] 20 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">INFO: [hmmsearch] 39 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">INFO: [hmmsearch] 59 of 194 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,6 +27,8 @@ INFO: [hmmsearch] 78 of 194 task(s) completed</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">INFO: [hmmsearch] 97 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">INFO: [hmmsearch] 117 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">INFO: [hmmsearch] 136 of 194 task(s) completed</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">INFO: [hmmsearch] 156 of 194 task(s) completed</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">INFO: [hmmsearch] 156 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">INFO: [hmmsearch] 175 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">INFO: [hmmsearch] 194 of 194 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">INFO: Results: C:1.0%[S:1.0%,D:0.0%],F:0.5%,M:98.5%,n:194 </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +39,7 @@ INFO: Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2019-06-26</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">INFO: ***** Run Prodigal on input to predict and extract genes *****</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">INFO: Genetic code 11 selected as optimal</span>
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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">INFO: Running 124 job(s) on hmmsearch</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">INFO: Running 124 job(s) on hmmsearch<span class="idiff left right">, starting at 07/01/2020 17:20:45</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">INFO: [hmmsearch] 13 of 124 task(s) completed</span>
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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">INFO: [hmmsearch] 25 of 124 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">INFO: [hmmsearch] 38 of 124 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" 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="56" 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">@@ -54,15 +56,15 @@ INFO: Results: C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">INFO: Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/eukaryota_odb10.2019-11-20.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">INFO: Decompressing file '/busco_wd/busco_downloads/lineages/eukaryota_odb10.tar.gz'</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">INFO: Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2019-11-20)</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">INFO: Running 1 job(s) on makeblastdb, starting at 07/01/2020 17:20:48</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">INFO: Creating BLAST database with input file</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">INFO: Running 1 job(s) on makeblastdb</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">INFO: [makeblastdb] 1 of 1 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">INFO: Running a BLAST search for BUSCOs against created database</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn<span class="idiff left right">, starting at 07/01/2020 17:20:48</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">INFO: [tblastn] 1 of 1 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">INFO: Running Augustus gene predictor on BLAST search results.</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">INFO: Running Augustus prediction using fly as species:</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">INFO: Running 52 job(s) on augustus</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">INFO: Running 52 job(s) on augustus<span class="idiff left right">, starting at 07/01/2020 17:20:48</span></span>
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66
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">INFO: [augustus] 6 of 52 task(s) completed</span>
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67
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">INFO: [augustus] 11 of 52 task(s) completed</span>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">INFO: [augustus] 16 of 52 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" 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="77" 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">@@ -75,7 +77,7 @@ INFO: [augustus] 47 of 52 task(s) completed</td>
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75
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">INFO: [augustus] 52 of 52 task(s) completed</span>
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76
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">INFO: Extracting predicted proteins...</span>
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77
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<td class="diff-line-num new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">INFO: Running 50 job(s) on hmmsearch</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">INFO: Running 50 job(s) on hmmsearch<span class="idiff left right">, starting at 07/01/2020 17:21:44</span></span>
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79
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">INFO: [hmmsearch] 5 of 50 task(s) completed</span>
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80
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">INFO: [hmmsearch] 10 of 50 task(s) completed</span>
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81
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">INFO: [hmmsearch] 15 of 50 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="93" 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">@@ -91,10 +93,10 @@ INFO: Results: C:15.3%[S:15.3%,D:0.0%],F:1.2%,M:83.5%,n:255</td>
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91
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">INFO: Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.</span>
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92
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">INFO: Extracting missing and fragmented buscos from the file ancestral_variants...</span>
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93
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">INFO: Running a BLAST search for BUSCOs against created database</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn, starting at 07/01/2020 17:21:45</span>
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94
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">INFO: [tblastn] 1 of 1 task(s) completed</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">INFO: Training Augustus using Single-Copy Complete BUSCOs:</span>
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96
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">INFO: Converting predicted genes to short genbank files</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">INFO: Running 39 job(s) on gff2gbSmallDNA.pl</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">INFO: Running 39 job(s) on gff2gbSmallDNA.pl<span class="idiff left right">, starting at 07/01/2020 17:21:49</span></span>
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98
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 4 of 39 task(s) completed</span>
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99
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 8 of 39 task(s) completed</span>
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100
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 12 of 39 task(s) completed</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">@@ -105,14 +107,15 @@ INFO: [gff2gbSmallDNA.pl] 28 of 39 task(s) completed</td>
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105
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 32 of 39 task(s) completed</span>
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106
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 36 of 39 task(s) completed</span>
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107
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 39 of 39 task(s) completed</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">INFO: All files converted to short genbank files, now <span class="idiff left right">running the training script</span>s</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext">INFO: Running 1 job(s) on new_species.pl</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">INFO: All files converted to short genbank files, now <span class="idiff left right">training Augustus using Single-Copy Complete BUSCO</span>s</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">INFO: Running 1 job(s) on new_species.pl<span class="idiff left right">, starting at 07/01/2020 17:21:49</span></span>
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110
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext">INFO: [new_species.pl] 1 of 1 task(s) completed</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">INFO: Running 1 job(s) on etraining</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">INFO: Running 1 job(s) on etraining<span class="idiff left right">, starting at 07/01/2020 17:21:50</span></span>
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112
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">INFO: [etraining] 1 of 1 task(s) completed</span>
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113
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">INFO: Re-running Augustus with the new metaparameters, number of target BUSCOs: 216</span>
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114
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">INFO: Running Augustus gene predictor on BLAST search results.</span>
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115
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">INFO: Running Augustus prediction using BUSCO_test_eukaryota as species:</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">INFO: Running 39 job(s) on augustus, starting at 07/01/2020 17:21:50</span>
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116
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">INFO: [augustus] 4 of 39 task(s) completed</span>
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117
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">INFO: [augustus] 8 of 39 task(s) completed</span>
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118
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">INFO: [augustus] 12 of 39 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" 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="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -125,17 +128,18 @@ INFO: [augustus] 36 of 39 task(s) completed</td>
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125
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext">INFO: [augustus] 39 of 39 task(s) completed</span>
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126
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext">INFO: Extracting predicted proteins...</span>
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127
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">INFO: [hmmsearch] 4 of 37 task(s) completed</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext">INFO: [hmmsearch] 8 of 37 task(s) completed</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">INFO: [hmmsearch] 12 of 37 task(s) completed</span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">INFO: [hmmsearch] 15 of 37 task(s) completed</span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">INFO: [hmmsearch] 19 of 37 task(s) completed</span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">INFO: [hmmsearch] 23 of 37 task(s) completed</span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">INFO: [hmmsearch] 26 of 37 task(s) completed</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">INFO: [hmmsearch] 30 of 37 task(s) completed</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">INFO: [hmmsearch] 34 of 37 task(s) completed</span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext">INFO: [hmmsearch] 37 of 37 task(s) completed</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">INFO: Results: C:18.8%[S:18.8%,D:0.0%],F:0.4%,M:80.8%,n:255 </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">INFO: Running 34 job(s) on hmmsearch, starting at 07/01/2020 17:22:01</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">INFO: [hmmsearch] 4 of 34 task(s) completed</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">INFO: [hmmsearch] 7 of 34 task(s) completed</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">INFO: [hmmsearch] 11 of 34 task(s) completed</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">INFO: [hmmsearch] 14 of 34 task(s) completed</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">INFO: [hmmsearch] 17 of 34 task(s) completed</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">INFO: [hmmsearch] 21 of 34 task(s) completed</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">INFO: [hmmsearch] 24 of 34 task(s) completed</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">INFO: [hmmsearch] 28 of 34 task(s) completed</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">INFO: [hmmsearch] 31 of 34 task(s) completed</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">INFO: [hmmsearch] 34 of 34 task(s) completed</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">INFO: Results: C:18.8%[S:18.8%,D:0.0%],F:1.2%,M:80.0%,n:255 </span>
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139
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"></span>
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140
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext">INFO: eukaryota_odb10 selected</span>
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141
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -155,18 +159,18 @@ INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxi</td>
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155
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext">INFO: Downloading file 'https://busco-data.ezlab.org/v4/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'</span>
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156
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext">INFO: Decompressing file '/busco_wd/busco_downloads/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'</span>
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157
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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext">INFO: Place the markers on the reference tree...</span>
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158
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<td class="diff-line-num new_line old" data-linenumber="162" 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="LC158" class="line" lang="plaintext">INFO: Running 1 job(s) on sepp</span>
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<td class="diff-line-num new old_line" data-linenumber="159" 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="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">INFO: Running 1 job(s) on sepp<span class="idiff left right">, starting at 07/01/2020 17:22:02</span></span>
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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
159
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<td class="diff-line-num new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext">INFO: [sepp] 1 of 1 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
160
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<td class="diff-line-num new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext">INFO: Lineage saccharomycetes is selected, supported by 16 markers out of 17</span>
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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
161
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<td class="diff-line-num new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext">INFO: Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/saccharomycetes_odb10.2019-11-20.tar.gz'</span>
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162
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<td class="diff-line-num new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext">INFO: Decompressing file '/busco_wd/busco_downloads/lineages/saccharomycetes_odb10.tar.gz'</span>
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163
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<td class="diff-line-num new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">INFO: Running BUSCO using lineage dataset saccharomycetes_odb10 (eukaryota, 2019-11-20)</span>
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<td class="diff-line-num old_line" data-linenumber="164" 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">
164
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<td class="diff-line-num new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">INFO: Running a BLAST search for BUSCOs against created database</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn</span>
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<td class="diff-line-num new old_line" data-linenumber="166" 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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn<span class="idiff left right">, starting at 07/01/2020 17:25:10</span></span>
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166
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<td class="diff-line-num new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext">INFO: [tblastn] 1 of 1 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="167" 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">
167
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<td class="diff-line-num new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext">INFO: Running Augustus gene predictor on BLAST search results.</span>
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<td class="diff-line-num old_line" data-linenumber="168" 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">
168
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<td class="diff-line-num new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext">INFO: Running Augustus prediction using aspergillus_nidulans as species:</span>
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169
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<td class="diff-line-num new_line old" data-linenumber="173" 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="LC169" class="line" lang="plaintext">INFO: Running 98 job(s) on augustus</span>
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<td class="diff-line-num new old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">INFO: Running 98 job(s) on augustus<span class="idiff left right">, starting at 07/01/2020 17:25:14</span></span>
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170
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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="plaintext">INFO: [augustus] 10 of 98 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="171" 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">
171
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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext">INFO: [augustus] 20 of 98 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="172" 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">
172
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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext">INFO: [augustus] 30 of 98 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="179" 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="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -179,7 +183,7 @@ INFO: [augustus] 89 of 98 task(s) completed</td>
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179
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext">INFO: [augustus] 98 of 98 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="180" 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">
180
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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext">INFO: Extracting predicted proteins...</span>
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<td class="diff-line-num old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
181
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<td class="diff-line-num new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<td class="diff-line-num new_line old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext">INFO: Running 63 job(s) on hmmsearch</span>
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<td class="diff-line-num new old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">INFO: Running 63 job(s) on hmmsearch<span class="idiff left right">, starting at 07/01/2020 17:25:54</span></span>
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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<td class="diff-line-num new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="plaintext">INFO: [hmmsearch] 7 of 63 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="plaintext">INFO: [hmmsearch] 13 of 63 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="185" 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">
185
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<td class="diff-line-num new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="plaintext">INFO: [hmmsearch] 19 of 63 task(s) completed</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -193,10 +197,10 @@ INFO: [hmmsearch] 63 of 63 task(s) completed</td>
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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
193
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<td class="diff-line-num new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="plaintext">INFO: Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="194" 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">
194
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<td class="diff-line-num new_line" data-linenumber="198" 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">
198
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC198" class="line" lang="plaintext">INFO: Extracting missing and fragmented buscos from the file ancestral_variants...</span>
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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<td class="diff-line-num new_line" data-linenumber="199" 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">
199
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext">INFO: Running a BLAST search for BUSCOs against created database</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="196" 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="200" 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">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">INFO: Running 1 job(s) on tblastn, starting at 07/01/2020 17:26:02</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
196
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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext">INFO: [tblastn] 1 of 1 task(s) completed</span>
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<td class="diff-line-num old old_line" data-linenumber="197" 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">
197
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<td class="diff-line-num new_line old" data-linenumber="202" 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="LC197" class="line" lang="plaintext">INFO: Training Augustus using Single-Copy Complete BUSCOs:</span>
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<td class="diff-line-num old_line" data-linenumber="198" 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">
198
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<td class="diff-line-num new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext">INFO: Converting predicted genes to short genbank files</span>
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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">INFO: Running 29 job(s) on gff2gbSmallDNA.pl</span>
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<td class="diff-line-num new old_line" data-linenumber="200" 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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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">INFO: Running 29 job(s) on gff2gbSmallDNA.pl<span class="idiff left right">, starting at 07/01/2020 17:27:08</span></span>
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200
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<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 3 of 29 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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<td class="diff-line-num new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 6 of 29 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
202
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<td class="diff-line-num new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 9 of 29 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" 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="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,14 +211,16 @@ INFO: [gff2gbSmallDNA.pl] 21 of 29 task(s) completed</td>
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207
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<td class="diff-line-num new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 24 of 29 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
208
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<td class="diff-line-num new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 27 of 29 task(s) completed</span>
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<td class="diff-line-num old_line" data-linenumber="209" 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">
209
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<td class="diff-line-num new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 29 of 29 task(s) completed</span>
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<td class="diff-line-num old old_line" data-linenumber="210" 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">
210
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<td class="diff-line-num new_line old" data-linenumber="214" 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="LC210" class="line" lang="plaintext">INFO: All files converted to short genbank files, now running the training scripts</span>
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<td class="diff-line-num old old_line" data-linenumber="211" 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">
211
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<td class="diff-line-num new_line old" data-linenumber="214" 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="LC211" class="line" lang="plaintext">INFO: Running 1 job(s) on new_species.pl</span>
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<td class="diff-line-num new old_line" data-linenumber="212" 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="214" 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">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">INFO: [gff2gbSmallDNA.pl] 29 of 29 task(s) completed</span>
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<td class="diff-line-num new old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">INFO: All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs</span>
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<td class="diff-line-num new old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">INFO: Running 1 job(s) on new_species.pl, starting at 07/01/2020 17:27:09</span>
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212
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">INFO: [new_species.pl] 1 of 1 task(s) completed</span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext">INFO: Running 1 job(s) on etraining</span>
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<td class="diff-line-num new old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">INFO: Running 1 job(s) on etraining<span class="idiff left right">, starting at 07/01/2020 17:27:09</span></span>
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214
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext">INFO: [etraining] 1 of 1 task(s) completed</span>
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215
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext">INFO: Re-running Augustus with the new metaparameters, number of target BUSCOs: 2108</span>
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<td class="diff-line-num old_line" data-linenumber="216" 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">
216
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<td class="diff-line-num new_line" data-linenumber="221" 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">
221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext">INFO: Running Augustus gene predictor on BLAST search results.</span>
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<td class="diff-line-num old_line" data-linenumber="217" 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">
217
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext">INFO: Running Augustus prediction using BUSCO_test_eukaryota as species:</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">INFO: Running 147 job(s) on augustus, starting at 07/01/2020 17:27:10</span>
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218
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="plaintext">INFO: [augustus] 15 of 147 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="plaintext">INFO: [augustus] 30 of 147 task(s) completed</span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="plaintext">INFO: [augustus] 45 of 147 task(s) completed</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="227" 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="233" 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">@@ -227,42 +233,45 @@ INFO: [augustus] 133 of 147 task(s) completed</td>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="plaintext">INFO: [augustus] 147 of 147 task(s) completed</span>
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228
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="plaintext">INFO: Extracting predicted proteins...</span>
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<td class="diff-line-num old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="plaintext">INFO: ***** Run HMMER on gene sequences *****</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext">INFO: [hmmsearch] 15 of 144 task(s) completed</span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="plaintext">INFO: [hmmsearch] 29 of 144 task(s) completed</span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="plaintext">INFO: [hmmsearch] 44 of 144 task(s) completed</span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext">INFO: [hmmsearch] 58 of 144 task(s) completed</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext">INFO: [hmmsearch] 73 of 144 task(s) completed</span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="plaintext">INFO: [hmmsearch] 116 of 144 task(s) completed</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext">INFO: [hmmsearch] 130 of 144 task(s) completed</span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="plaintext">INFO: [hmmsearch] 144 of 144 task(s) completed</span>
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<td class="diff-line-num old old_line" data-linenumber="238" 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="LC238" class="line" lang="plaintext">INFO: Results: C:2.0%[S:2.0%,D:0.0%],F:0.1%,M:97.9%,n:2137 </span>
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<td class="diff-line-num new old_line" data-linenumber="239" 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="LC236" class="line" lang="plaintext">INFO: Running 140 job(s) on hmmsearch, starting at 07/01/2020 17:27:58</span>
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<td class="diff-line-num new old_line" data-linenumber="239" 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="LC237" class="line" lang="plaintext">INFO: [hmmsearch] 14 of 140 task(s) completed</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">INFO: [hmmsearch] 28 of 140 task(s) completed</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">INFO: [hmmsearch] 42 of 140 task(s) completed</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">INFO: [hmmsearch] 56 of 140 task(s) completed</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">INFO: [hmmsearch] 70 of 140 task(s) completed</span>
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<td class="diff-line-num new new_line" data-linenumber="242" 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">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">INFO: [hmmsearch] 84 of 140 task(s) completed</span>
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<td class="diff-line-num new new_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">INFO: [hmmsearch] 98 of 140 task(s) completed</span>
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<td class="diff-line-num new old_line" data-linenumber="239" 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="244" 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">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">INFO: [hmmsearch] 112 of 140 task(s) completed</span>
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<td class="diff-line-num new old_line" data-linenumber="239" 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="245" 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">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">INFO: [hmmsearch] 126 of 140 task(s) completed</span>
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<td class="diff-line-num new old_line" data-linenumber="239" 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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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">INFO: [hmmsearch] 140 of 140 task(s) completed</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">INFO: Results: C:2.0%[S:2.0%,D:0.0%],F:0.3%,M:97.7%,n:2137 </span>
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239
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext"></span>
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240
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext">INFO: </span>
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241
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"></span>
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242
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext"> --------------------------------------------------</span>
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243
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext"> |Results from generic domain eukaryota_odb10 |</span>
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244
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<td class="diff-line-num new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="plaintext"> --------------------------------------------------</span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="plaintext"> |C:18.8%[S:18.8%,D:0.0%],F:<span class="idiff left right">0.4%,M:80.8</span>%,n:255 |</span>
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<td class="diff-line-num new old_line" data-linenumber="246" 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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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> |C:18.8%[S:18.8%,D:0.0%],F:<span class="idiff left right">1.2%,M:80.0</span>%,n:255 |</span>
</pre>
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246
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext"> |48 Complete BUSCOs (C) |</span>
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<td class="diff-line-num old_line" data-linenumber="247" 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">
247
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<td class="diff-line-num new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext"> |48 Complete and single-copy BUSCOs (S) |</span>
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<td class="diff-line-num old_line" data-linenumber="248" 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">
248
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<td class="diff-line-num new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="plaintext"> |0 Complete and duplicated BUSCOs (D) |</span>
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249
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<td class="diff-line-num new_line old" data-linenumber="258" 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="LC249" class="line" lang="plaintext"> |<span class="idiff left right">1</span> Fragmented BUSCOs (F) |</span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="plaintext"> |20<span class="idiff left right">6</span> Missing BUSCOs (M) |</span>
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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> |<span class="idiff left right">3</span> Fragmented BUSCOs (F) |</span>
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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> |20<span class="idiff left right">4</span> Missing BUSCOs (M) |</span>
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<td class="diff-line-num old_line" data-linenumber="251" 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">
251
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<td class="diff-line-num new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext"> |255 Total BUSCO groups searched |</span>
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252
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="plaintext"> --------------------------------------------------</span>
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253
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="plaintext"></span>
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254
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"> --------------------------------------------------</span>
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255
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext"> |Results from dataset saccharomycetes_odb10 |</span>
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<td class="diff-line-num old_line" data-linenumber="256" 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">
256
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"> --------------------------------------------------</span>
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<td class="diff-line-num old old_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="plaintext"> |C:2.0%[S:2.0%,D:0.0%],F:0.<span class="idiff left right">1%,M:97.9</span>%,n:2137 |</span>
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<td class="diff-line-num new old_line" data-linenumber="258" 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="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> |C:2.0%[S:2.0%,D:0.0%],F:0.<span class="idiff left right">3%,M:97.7</span>%,n:2137 |</span>
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<td class="diff-line-num old_line" data-linenumber="258" 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">
258
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"> |42 Complete BUSCOs (C) |</span>
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<td class="diff-line-num old_line" data-linenumber="259" 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">
259
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<td class="diff-line-num new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"> |42 Complete and single-copy BUSCOs (S) |</span>
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260
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext"> |0 Complete and duplicated BUSCOs (D) |</span>
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261
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<td class="diff-line-num new_line old" data-linenumber="270" 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="LC261" class="line" lang="plaintext"> |<span class="idiff left right">3</span> Fragmented BUSCOs (F) |</span>
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<td class="diff-line-num old old_line" data-linenumber="262" 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">
262
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<td class="diff-line-num new_line old" data-linenumber="270" 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="LC262" class="line" lang="plaintext"> |20<span class="idiff left right">92</span> Missing BUSCOs (M) |</span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> |<span class="idiff left right">6</span> Fragmented BUSCOs (F) |</span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> |20<span class="idiff left right">89</span> Missing BUSCOs (M) |</span>
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263
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="plaintext"> |2137 Total BUSCO groups searched |</span>
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264
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<td class="diff-line-num new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="plaintext"> --------------------------------------------------</span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="plaintext">INFO: BUSCO analysis done with WARNING(s). Total running time: <span class="idiff left right">212</span> seconds</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">INFO: BUSCO analysis done with WARNING(s). Total running time: <span class="idiff left right">440</span> seconds</span>
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266
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="267" 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">
267
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext">***** Summary of warnings: *****</span>
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<td class="diff-line-num old_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="plaintext">WARNING:busco.ConfigManager Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line.</span>
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