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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/busco">Debian Med / busco</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/eb09048fc060132e5d156eee522dc541bdc8fd0a">eb09048f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-25T19:57:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.2.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/b82e77eaa16ed19c7b4315039ca93426e7163942">b82e77ea</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-25T19:57:09+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.2.2'
Update to upstream version '5.2.2'
with Debian dir 60bf48fbfcfc448b6af6a472c445470864626fb7</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/851f7574d4f96da0433d053b4c22c087ddb43f82">851f7574</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-25T20:00:00+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/busco/-/commit/d72823781030d21c44d37fbb82e024b717d2742b">d7282378</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-25T20:01:04+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
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<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
CHANGELOG
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#e8c92be72798d359b194a6dae2d7a90f61fe681a">
debian/patches/fix-and-disable-tests.patch
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<li class="file-stats">
<a href="#de7754708bf8aa012a49a842a0d52b6628af3d59">
src/busco/AutoLineage.py
</a>
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<li class="file-stats">
<a href="#e497bbf996017c0692c161d2cfed28374276cc73">
src/busco/BuscoConfig.py
</a>
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<li class="file-stats">
<a href="#a8fd6f8fc327bd92758f2c1e85bd45f1bad18df0">
src/busco/BuscoRunner.py
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<li class="file-stats">
<a href="#ba1a56246dbcc4652eb6c8edd5d818e5b5c81d88">
src/busco/_version.py
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<li class="file-stats">
<a href="#cf0fa70998d90d794d0bbb251526f730829daf8b">
src/busco/analysis/BuscoAnalysis.py
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<li class="file-stats">
<a href="#0750dd8caad8daa319bd078a0d80872708eb7fa7">
src/busco/analysis/GenomeAnalysis.py
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<li class="file-stats">
<a href="#9d54a8efc4f30849596104b53c7b5221e320b1c7">
src/busco/busco_tools/Toolset.py
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<li class="file-stats">
<a href="#a5f82d71f925534007d3cb3b900ad8be00859451">
src/busco/busco_tools/hmmer.py
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<li class="file-stats">
<a href="#bd0e703ba072ee7447fcc5bd1e634475b3438cf9">
src/busco/run_BUSCO.py
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</li>
<li class="file-stats">
<a href="#4d3a9839ba0a4f2cc537e69c146c7eb84ae0a7a7">
tests/unittests/BuscoConfig_unittests.py
</a>
</li>
<li class="file-stats">
<a href="#aa012e22a56237f02b563d02f1158f5cb5ac25fe">
tests/unittests/run_BUSCO_unittests.py
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</ul>
<h4>Changes:</h4>
<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">
<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">5.2.2</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">- Issue #390 fixed</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">- Issue #423 fixed</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">- Issue #464 fixed</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">- Issue #467 fixed</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">- Issue #470 fixed</span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">- Add --tar option to compress some output folders</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">5.2.1</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">- Minor bug fixes</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">busco (5.2.<span class="idiff left right">1</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">busco (5.2.<span class="idiff left right">2</span>-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * New upstream version 5.2.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version 5.2.<span class="idiff left right">2</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Update manpage</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Install config.ini file as an example</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Add Depends on python3-biopython and python3-pandas</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">@@ -8,7 +8,7 @@ busco (5.2.1-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * d/p/fix-and-disable-tests.patch: Add patch to fix test execution</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> <span class="idiff left">Fri, 09</span> Jul 2021 <span class="idiff right">22:09:38</span> +0530</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> <span class="idiff left">Sun, 25</span> Jul 2021 <span class="idiff right">19:57:23</span> +0530</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">busco (5.0.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<li id="e8c92be72798d359b194a6dae2d7a90f61fe681a">
<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#e8c92be72798d359b194a6dae2d7a90f61fe681a"><strong>debian/patches/fix-and-disable-tests.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> self, mock_config_manager, fake_modedict, mock_cleanup, *args</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/unittests/BuscoConfig_unittests.py</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/unittests/BuscoConfig_unittests.py</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="p">@@ -35<span class="idiff left">3</span>,7 +35<span class="idiff right">3</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -35<span class="idiff left">5</span>,7 +35<span class="idiff right">5</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> config.configure()</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> config._check_evalue()</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> def test_evalue_default(self, mock_logger):</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> self.test_params["evalue"] = 0.001</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">399</span>,7 +<span class="idiff right">399</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">401</span>,7 +<span class="idiff right">401</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> @patch(</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">@@ -91,7 +91,7 @@ Last-Update: 2021-07-02</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"> def test_batch_mode_true(self, *args):</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="diff"> config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left">09</span>,10 +4<span class="idiff right">09</span>,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left">11</span>,10 +4<span class="idiff right">11</span>,10 @@</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> config.set.assert_has_calls(calls)</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="diff"> @patch(</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">@@ -104,7 +104,7 @@ Last-Update: 2021-07-02</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="diff"> def test_batch_mode_false_with_file(self, *args):</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="p">@@ -42<span class="idiff left">0</span>,10 +42<span class="idiff right">0</span>,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="p">@@ -42<span class="idiff left">2</span>,10 +42<span class="idiff right">2</span>,10 @@</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"> config._check_batch_mode()</span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"> @patch(</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 +117,7 @@ Last-Update: 2021-07-02</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> def test_batch_mode_false_with_error(self, *args):</span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> config = BuscoConfig.BuscoConfigMain(self.base_config, self.test_params)</span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="p">@@ -44<span class="idiff left">1</span>,14 +44<span class="idiff right">1</span>,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -44<span class="idiff left">3</span>,14 +44<span class="idiff right">3</span>,14 @@</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"> with self.assertRaises(BuscoConfig.BatchFatalError):</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="diff"> config._check_required_input_exists()</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#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">@@ -84,7 +84,7 @@ class AutoSelectLineage:</td>
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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="LC85" 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="LC86" 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="LC87" 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;">virus_check</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;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">virus_check</span><span class="p">()</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</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">config</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getboolean</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">"auto-lineage-euk"</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">virus_pipeline</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="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">run_virus_datasets</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC90" 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="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;">runners</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">@@ -135,7 +135,7 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">max_ind</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inds</span><span class="p">[</span><span class="n" style="color: #333;">max_mask</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;">return</span> <span class="n" style="color: #333;">max_ind</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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">evaluate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">runners</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;">evaluate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">runners</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_percent</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"><span class="s" style="color: #d14;"> Evaluate output scores from all BUSCO runs. Lineage with the highest number of complete (single + multiple)</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;"> copy BUSCOs is assigned as the best_match_lineage.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(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="147" style="width: 35px; color: rgba(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">@@ -147,9 +147,9 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">collate_results</span><span class="p">(</span><span class="n" style="color: #333;">runners</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">max_ind</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_max_ind</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><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>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">max_ind</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">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_max_ind</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</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">s_percents</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="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</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">d_percents</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_percent</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</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;">get_max_ind</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><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>
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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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">max_ind</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="LC152" class="line" lang="python"> <span class="n" style="color: #333;">max_ind2</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_max_ind</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><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;">max_ind</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">max_ind2</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">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_max_ind</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">array</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">f_percents</span></span><span class="p"><span class="idiff">)[</span></span><span class="n" style="color: #333;"><span class="idiff">max_ind</span></span><span class="p"><span class="idiff">])</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_percent</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</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;">get_max_ind</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">(</span><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;">max_ind</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;">max_ind</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_ind</span><span class="p">[</span><span class="n" style="color: #333;">max_ind2</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC154" 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;">max_ind</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="LC155" 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;">s_buscos</span><span class="p">[</span><span class="n" style="color: #333;">max_ind</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="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -170,10 +170,12 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC170" 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;">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_runner</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy</span> <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;">runners</span><span class="p">]</span></span>
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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;">f_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><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;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">only_fragments</span> <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;">runners</span><span class="p">]</span></span>
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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;">s_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><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;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">s_percent</span> <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;">runners</span><span class="p">]</span></span>
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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;">d_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><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;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">d_percent</span> <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;">runners</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;">f_percents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><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;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">f_percent</span> <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;">runners</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;">return</span></span>
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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="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_best_match_lineage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">runners</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">max_ind</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;">evaluate</span><span class="p">(</span><span class="n" style="color: #333;">runners</span><span class="p">)</span></span>
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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;">get_best_match_lineage</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">runners</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_percent</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">max_ind</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;">evaluate</span><span class="p">(</span><span class="n" style="color: #333;">runners</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">use_percent</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC179" 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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runners</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">max_ind</span><span class="p">)]</span></span>
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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;">best_match_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;">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>
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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="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">max_ind</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -199,7 +201,8 @@ class AutoSelectLineage:</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="s" style="color: #d14;">"Certain mollicute clades use a different genetic code to the rest of bacteria. They are not part "</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="s" style="color: #d14;">"of the BUSCO placement tree and need to be tested separately. For more information, see the user "</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="s" style="color: #d14;">"guide."</span><span class="p">)</span></span>
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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;">check_mollicutes</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;">use_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;">selected_runner</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>
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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;">check_mollicutes</span><span class="p">(</span><span class="n" style="color: #333;">use_percent</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;">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;">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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<pre style="margin: 0;"> <span id="LC207" 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;">"Bacteria domain is a better match than the mollicutes subclade. Continuing to tree placement."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC208" 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">@@ -223,10 +226,10 @@ class AutoSelectLineage:</td>
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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;">set_best_match_lineage</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="LC227" class="line" lang="python"> <span class="n" style="color: #333;">AnalysisRunner</span><span class="p">.</span><span class="n" style="color: #333;">selected_dataset</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;">best_match_lineage_dataset</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC228" 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;">check_mollicutes</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="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_mollicutes</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">use_percent</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC230" 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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231
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<pre style="margin: 0;"> <span id="LC231" 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="LC229" 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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<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;">get_best_match_lineage</span><span class="p">(</span><span class="n" style="color: #333;">runners</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">use_percent</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">use_percent</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_busco_placer</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: revisit structure of this method after cleaning BuscoPlacer</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#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">@@ -36,6 +36,7 @@ class BaseConfig(ConfigParser):</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"use_augustus"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"long"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"batch_mode"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"tar"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">DEPENDENCY_SECTIONS</span> <span class="o" style="font-weight: 600;">=</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">@@ -79,6 +80,7 @@ class BaseConfig(ConfigParser):</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">"limit"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="s" style="color: #d14;">"use_augustus"</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;">"batch_mode"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"tar"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <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="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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -682,16 +684,9 @@ class BuscoConfigMain(BuscoConfig, BaseConfig):</td>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_value_constraints</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="LC686" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python"><span class="s" style="color: #d14;"> Load default values into config if not provided in config file or on the command line.</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="python"><span class="s" style="color: #d14;"> :return:</span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for param in list(type(self).DEFAULT_ARGS_VALUES.keys()):</span></span>
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<pre style="margin: 0;">-<span id="LC689" 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="LC690" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.get("busco_run", param)</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># except NoOptionError:</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># self.set("busco_run", param, str(type(self).DEFAULT_ARGS_VALUES[param]))</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Set auto-lineage to True if either auto-lineage-prok or auto-lineage-euk is selected</span></span>
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<pre style="margin: 0;"> <span id="LC690" 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;">"auto-lineage-prok"</span><span class="p">)</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;">getboolean</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"> <span class="s" style="color: #d14;">"busco_run"</span><span class="p">,</span> <span class="s" style="color: #d14;">"auto-lineage-euk"</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#a8fd6f8fc327bd92758f2c1e85bd45f1bad18df0"><strong>src/busco/BuscoRunner.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">@@ -28,6 +28,9 @@ logger = BuscoLogger.get_logger(__name__)</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleRunner</span><span class="p">:</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="LC32" class="line" lang="python"> <span class="n" style="color: #333;">all_runners</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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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;">config_manager</span><span class="p">):</span></span>
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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;">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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<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;">config_manager</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">config_manager</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">@@ -65,6 +68,7 @@ class SingleRunner:</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">asl</span><span class="p">.</span><span class="n" style="color: #333;">set_best_match_lineage</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">lineage_dataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">asl</span><span class="p">.</span><span class="n" style="color: #333;">best_match_lineage_dataset</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">asl</span><span class="p">.</span><span class="n" style="color: #333;">selected_runner</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <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;">all_runners</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">asl</span><span class="p">.</span><span class="n" style="color: #333;">runners</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;">asl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">()</span></span>
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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;">lineage_dataset</span><span class="p">,</span> <span class="n" style="color: #333;">runner</span></span>
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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">@@ -121,10 +125,13 @@ class SingleRunner:</td>
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<pre style="margin: 0;"> <span id="LC125" 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="LC126" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">runner</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="LC127" class="line" lang="python"> <span class="n" style="color: #333;">AnalysisRunner</span><span class="p">.</span><span class="n" style="color: #333;">selected_dataset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage_basename</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <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;">all_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;">runner</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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130
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<pre style="margin: 0;">+<span id="LC130" 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;">"tar"</span><span class="p">):</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">compress_folders</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">runner</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">start_time</span><span class="p">)</span></span>
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125
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">BuscoError</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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127
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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;">log_error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">BuscoError</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="k" style="font-weight: 600;">raise</span></span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC137" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(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">@@ -147,6 +154,34 @@ class SingleRunner:</td>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">BatchFatalError</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">compress_folders</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="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="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;">all_runners</span><span class="p">:</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">folders_to_compress</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="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;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">single_copy_sequences_folder</span><span class="p">,</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">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_runner</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy_sequences_folder</span><span class="p">,</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">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_runner</span><span class="p">.</span><span class="n" style="color: #333;">fragmented_sequences_folder</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;">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_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_folder</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="p">]</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">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;">"use_augustus"</span><span class="p">):</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">folders_to_compress</span><span class="p">.</span><span class="n" style="color: #333;">append</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;">runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">pred_genes_dir_initial</span><span class="p">,</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">pred_genes_dir_rerun</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;">runner</span><span class="p">.</span><span class="n" style="color: #333;">analysis</span><span class="p">.</span><span class="n" style="color: #333;">augustus_runner</span><span class="p">.</span><span class="n" style="color: #333;">gff_dir</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="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;">gff2gb_runner</span><span class="p">.</span><span class="n" style="color: #333;">gb_folder</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="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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">folder</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">folders_to_compress</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;">try</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;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">make_archive</span><span class="p">(</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">folder</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="s" style="color: #d14;">"gztar"</span><span class="p">,</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">),</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">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;">folder</span><span class="p">),</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">folder</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;">except</span> <span class="nb" style="color: #0086b3;">OSError</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;">raise</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># logger.warning("Unable to compress folder {}".format(folder))</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"></span>
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150
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BatchRunner</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>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -276,6 +311,8 @@ class AnalysisRunner:</td>
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276
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311
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<pre style="margin: 0;"> <span id="LC311" 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;">"prok_tran"</span></span>
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277
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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;">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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313
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<pre style="margin: 0;"> <span id="LC313" 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_tran"</span></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;">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;">"viruses"</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="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="c1" style="color: #998; font-style: italic;"># Suggested by Mose - Prodigal may perform better on viruses than BLAST + HMMER.</span></span>
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279
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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280
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">BatchFatalError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unrecognized mode {}"</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;">mode</span><span class="p">))</span></span>
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281
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -505,6 +542,10 @@ class AnalysisRunner:</td>
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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;">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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506
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543
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<pre style="margin: 0;"> <span id="LC543" 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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507
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544
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<pre style="margin: 0;"> <span id="LC544" 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;">auto_lineage_line</span><span class="p">)</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" 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>
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546
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<pre style="margin: 0;">+<span id="LC546" 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;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">short_summary_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"a"</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">short_summary_file</span><span class="p">:</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">short_summary_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">positive_parasitic_line</span><span class="p">)</span></span>
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python"></span>
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509
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550
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<pre style="margin: 0;"> <span id="LC550" 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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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#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) 2016-2021, 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;">"5.2.<span class="idiff left right">1</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;">"5.2.<span class="idiff left right">2</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#cf0fa70998d90d794d0bbb251526f730829daf8b"><strong>src/busco/analysis/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">@@ -119,6 +119,12 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="p">)</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;">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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<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 HMMER run as output already processed"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC122" 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;">restart</span> <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>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">"{}.tar.gz"</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;">hmmer_runner</span><span class="p">.</span><span class="n" style="color: #333;">output_folder</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">BuscoError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"Restart mode incompatible with a previously compressed (--tar) run. Please decompress the HMMER results folder and try again."</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</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;">results_dir</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="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">BuscoError</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="s" style="color: #d14;">"HMMER results directory not empty. If you are running in restart mode, make sure you are "</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -190,11 +196,14 @@ class BuscoAnalysis(metaclass=ABCMeta):</td>
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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;">_check_dataset_integrity</span><span class="p">()</span></span>
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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="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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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">BuscoError</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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<pre style="margin: 0;">-<span id="LC193" 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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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC195" 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="LC196" 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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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_seq_uniqueness</span><span class="p">(</span><span class="n" style="color: #333;">line</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="k" style="font-weight: 600;">try</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="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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201
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<pre style="margin: 0;">+<span id="LC201" 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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202
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<pre style="margin: 0;">+<span id="LC202" 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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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;">_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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204
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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;">_check_seq_uniqueness</span><span class="p">(</span><span class="n" style="color: #333;">line</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="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">UnicodeDecodeError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ude</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;">raise</span> <span class="n" style="color: #333;">BuscoError</span><span class="p">(</span><span class="n" style="color: #333;">ude</span><span class="p">.</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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198
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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;">return</span></span>
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199
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_seq_uniqueness</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">):</span></span>
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<li id="0750dd8caad8daa319bd078a0d80872708eb7fa7">
<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#0750dd8caad8daa319bd078a0d80872708eb7fa7"><strong>src/busco/analysis/GenomeAnalysis.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="586" style="width: 35px; color: rgba(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="586" style="width: 35px; color: rgba(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">@@ -586,8 +586,10 @@ class GenomeAnalysisEukaryotesMetaeuk(GenomeAnalysisEukaryotes):</td>
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586
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="python"> <span class="p">]</span></span>
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587
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hmmer_result_dict_new</span><span class="p">,</span> <span class="n" style="color: #333;">matched_genes_new</span></span>
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588
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC589" 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;">"Validating exons and removing overlapping matches"</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="LC589" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">exons_to_df</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC590" 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;">"genome"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC591" 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;">"Validating exons and removing overlapping matches"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"></span>
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">df</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;">metaeuk_runner</span><span class="p">.</span><span class="n" style="color: #333;">records_to_df</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">)</span></span>
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592
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Start"</span><span class="p">].</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Stop"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">df</span><span class="p">[</span><span class="s" style="color: #d14;">"Stop"</span><span class="p">].</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#9d54a8efc4f30849596104b53c7b5221e320b1c7"><strong>src/busco/busco_tools/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">@@ -69,7 +69,8 @@ class Job(Process):</td>
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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;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span></span>
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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;">cmd_line</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;">capture_output</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># stdout and stderr streams are stored and written to file after job completion</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># stdout and stderr streams are stored and written to file after job completion</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">cwd</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;">cwd</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;">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="LC76" class="line" lang="python"> <span class="n" style="color: #333;">timeout</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;">timeout</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#a5f82d71f925534007d3cb3b900ad8be00859451"><strong>src/busco/busco_tools/hmmer.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">@@ -101,6 +101,7 @@ class HMMERRunner(BaseRunner):</td>
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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;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mode</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">is_fragment</span> <span class="o" style="font-weight: 600;">=</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;">matched_genes_fragment</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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106
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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;">single_copy_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">multi_copy_buscos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#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">@@ -152,7 +152,8 @@ def _parse_args():</td>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SEQUENCE_FILE"</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;">"Input sequence file in FASTA format. "</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">"Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set."</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="s" style="color: #d14;">"Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. "</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">"Also possible to use a path to a directory containing multiple input files."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -385,6 +386,14 @@ def _parse_args():</td>
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">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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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="p">)</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="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="LC390" class="line" lang="python"> <span class="s" style="color: #d14;">"--tar"</span><span class="p">,</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"tar"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Compress some subdirectories with many files to save space"</span><span class="p">,</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="p">)</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"></span>
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388
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">optional</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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389
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="s" style="color: #d14;">"--update-data"</span><span class="p">,</span></span>
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390
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"update-data"</span><span class="p">,</span></span>
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<li id="4d3a9839ba0a4f2cc537e69c146c7eb84ae0a7a7">
<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#4d3a9839ba0a4f2cc537e69c146c7eb84ae0a7a7"><strong>tests/unittests/BuscoConfig_unittests.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,6 +43,7 @@ class TestBuscoConfig(unittest.TestCase):</td>
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43
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"download_path"</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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44
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"update-data"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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45
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="s" style="color: #d14;">"version"</span><span class="p">:</span> <span class="s" style="color: #d14;">"==SUPPRESS=="</span><span class="p">,</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="s" style="color: #d14;">"tar"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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46
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="p">}</span></span>
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47
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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48
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49
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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;">test_params</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(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="81" style="width: 35px; color: rgba(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">@@ -80,6 +81,7 @@ class TestBuscoConfig(unittest.TestCase):</td>
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80
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="s" style="color: #d14;">"limit"</span><span class="p">,</span></span>
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81
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">"use_augustus"</span><span class="p">,</span></span>
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82
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"batch_mode"</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="s" style="color: #d14;">"tar"</span><span class="p">,</span></span>
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83
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="p">],</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"etraining"</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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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"gff2gbSmallDNA.pl"</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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<a href="https://salsa.debian.org/med-team/busco/-/compare/f74f6e63cd60bc848648ddfe8e0878d152e7685b...d72823781030d21c44d37fbb82e024b717d2742b#aa012e22a56237f02b563d02f1158f5cb5ac25fe"><strong>tests/unittests/run_BUSCO_unittests.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">@@ -116,6 +116,7 @@ class TestParams(unittest.TestCase):</td>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"download_path"</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">"update-data"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">"version"</span><span class="p">:</span> <span class="s" style="color: #d14;">"==SUPPRESS=="</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="s" style="color: #d14;">"tar"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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119
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertDictEqual</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">correct_parse</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_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="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">@@ -173,6 +174,7 @@ class TestParams(unittest.TestCase):</td>
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173
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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;">"download_path"</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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174
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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;">"update-data"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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175
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="s" style="color: #d14;">"version"</span><span class="p">:</span> <span class="s" style="color: #d14;">"==SUPPRESS=="</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="s" style="color: #d14;">"tar"</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertDictEqual</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">correct_parse</span><span class="p">)</span></span>
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178
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -223,6 +225,7 @@ class TestParams(unittest.TestCase):</td>
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="s" style="color: #d14;">"--augustus"</span><span class="p">,</span></span>
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="s" style="color: #d14;">"--update-data"</span><span class="p">,</span></span>
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">"--offline"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="s" style="color: #d14;">"--tar"</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="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">command_str</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>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <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;">key</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">arg_values</span><span class="p">.</span><span class="n" style="color: #333;">items</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">@@ -261,6 +264,7 @@ class TestParams(unittest.TestCase):</td>
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261
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="s" style="color: #d14;">"quiet"</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="s" style="color: #d14;">"update-data"</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="LC266" class="line" lang="python"> <span class="s" style="color: #d14;">"version"</span><span class="p">:</span> <span class="s" style="color: #d14;">"==SUPPRESS=="</span><span class="p">,</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="s" style="color: #d14;">"tar"</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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264
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertDictEqual</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">correct_parse</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"></span>
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